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Publisher: Medknow Publishers   (Total: 179 journals)

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Journal of Pathology Informatics    Follow    
  This is an Open Access Journal Open Access journal
     ISSN (Print) 2153-3539 - ISSN (Online) 2153-3539
     Published by Medknow Publishers Homepage  [179 journals]
  • Mapping stain distribution in pathology slides using whole slide imaging
    • Authors: Fang-Cheng Yeh, Qing Ye, T Kevin Hitchens, Yijen L Wu, Anil V Parwani, Chien Ho
      Pages: 1 - 1
      Abstract: Fang-Cheng Yeh, Qing Ye, T Kevin Hitchens, Yijen L Wu, Anil V Parwani, Chien Ho

      Journal of Pathology Informatics 2014 5(1):1-1

      Background: Whole slide imaging (WSI) offers a novel approach to digitize and review pathology slides, but the voluminous data generated by this technology demand new computational methods for image analysis. Materials and Methods: In this study, we report a method that recognizes stains in WSI data and uses kernel density estimator to calculate the stain density across the digitized pathology slides. The validation study was conducted using a rat model of acute cardiac allograft rejection and another rat model of heart ischemia/reperfusion injury. Immunohistochemistry (IHC) was conducted to label ED1 + macrophages in the tissue sections and the stained slides were digitized by a whole slide scanner. The whole slide images were tessellated to enable parallel processing. Pixel-wise stain classification was conducted to classify the IHC stains from those of the background and the density distribution of the identified IHC stains was then calculated by the kernel density estimator. Results: The regression analysis showed a correlation coefficient of 0.8961 between the number of IHC stains counted by our stain recognition algorithm and that by the manual counting, suggesting that our stain recognition algorithm was in good agreement with the manual counting. The density distribution of the IHC stains showed a consistent pattern with those of the cellular magnetic resonance (MR) images that detected macrophages labeled by ultrasmall superparamagnetic iron-oxide or micron-sized iron-oxide particles. Conclusions: Our method provides a new imaging modality to facilitate clinical diagnosis. It also provides a way to validate/correlate cellular MRI data used for tracking immune-cell infiltration in cardiac transplant rejection and cardiac ischemic injury.
      Citation: Journal of Pathology Informatics 2014 5(1):1-1
      PubDate: Fri,31 Jan 2014
      DOI: 10.4103/2153-3539.126140
      Issue No: Vol. 5, No. 1 (2014)
       
  • The 2013 symposium on pathology data integration and clinical decision
           support and the current state of field
    • Authors: Jason M Baron, Anand S Dighe, Ramy Arnaout, Ulysses J Balis, W Stephen Black-Schaffer, Alexis B Carter, Walter H Henricks, John M Higgins, Brian R Jackson, JiYeon Kim, Veronica E Klepeis, Long P Le, David N Louis, Diana Mandelker, Craig H Mermel, James S Michaelson, Rakesh Nagarajan, Mihae E Platt, Andrew M Quinn, Luigi Rao, Brian H Shirts, John R Gilbertson
      Pages: 2 - 2
      Abstract: Jason M Baron, Anand S Dighe, Ramy Arnaout, Ulysses J Balis, W Stephen Black-Schaffer, Alexis B Carter, Walter H Henricks, John M Higgins, Brian R Jackson, JiYeon Kim, Veronica E Klepeis, Long P Le, David N Louis, Diana Mandelker, Craig H Mermel, James S Michaelson, Rakesh Nagarajan, Mihae E Platt, Andrew M Quinn, Luigi Rao, Brian H Shirts, John R Gilbertson

      Journal of Pathology Informatics 2014 5(1):2-2

      Background: Pathologists and informaticians are becoming increasingly interested in electronic clinical decision support for pathology, laboratory medicine and clinical diagnosis. Improved decision support may optimize laboratory test selection, improve test result interpretation and permit the extraction of enhanced diagnostic information from existing laboratory data. Nonetheless, the field of pathology decision support is still developing. To facilitate the exchange of ideas and preliminary studies, we convened a symposium entitled: Pathology data integration and clinical decision support. Methods: The symposium was held at the Massachusetts General Hospital, on May 10, 2013. Participants were selected to represent diverse backgrounds and interests and were from nine different institutions in eight different states. Results: The day included 16 plenary talks and three panel discussions, together covering four broad areas. Summaries of each presentation are included in this manuscript. Conclusions: A number of recurrent themes emerged from the symposium. Among the most pervasive was the dichotomy between diagnostic data and diagnostic information, including the opportunities that laboratories may have to use electronic systems and algorithms to convert the data they generate into more useful information. Differences between human talents and computer abilities were described; well-designed symbioses between humans and computers may ultimately optimize diagnosis. Another key theme related to the unique needs and challenges in providing decision support for genomics and other emerging diagnostic modalities. Finally, many talks relayed how the barriers to bringing decision support toward reality are primarily personnel, political, infrastructural and administrative challenges rather than technological limitations.
      Citation: Journal of Pathology Informatics 2014 5(1):2-2
      PubDate: Fri,31 Jan 2014
      DOI: 10.4103/2153-3539.126145
      Issue No: Vol. 5, No. 1 (2014)
       
  • Mining genome sequencing data to identify the genomic features linked to
           breast cancer histopathology
    • Authors: Zheng Ping, Gene P Siegal, Jonas S Almeida, Stuart J Schnitt, Dejun Shen
      Pages: 3 - 3
      Abstract: Zheng Ping, Gene P Siegal, Jonas S Almeida, Stuart J Schnitt, Dejun Shen

      Journal of Pathology Informatics 2014 5(1):3-3

      Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.
      Citation: Journal of Pathology Informatics 2014 5(1):3-3
      PubDate: Fri,31 Jan 2014
      DOI: 10.4103/2153-3539.126147
      Issue No: Vol. 5, No. 1 (2014)
       
  • Color standardization in whole slide imaging using a color calibration
           slide
    • Authors: Pinky A Bautista, Noriaki Hashimoto, Yukako Yagi
      Pages: 4 - 4
      Abstract: Pinky A Bautista, Noriaki Hashimoto, Yukako Yagi

      Journal of Pathology Informatics 2014 5(1):4-4

      Background: Color consistency in histology images is still an issue in digital pathology. Different imaging systems reproduced the colors of a histological slide differently. Materials and Methods: Color correction was implemented using the color information of the nine color patches of a color calibration slide. The inherent spectral colors of these patches along with their scanned colors were used to derive a color correction matrix whose coefficients were used to convert the pixels' colors to their target colors. Results: There was a significant reduction in the CIELAB color difference, between images of the same H & E histological slide produced by two different whole slide scanners by 3.42 units, P < 0.001 at 95% confidence level. Conclusion: Color variations in histological images brought about by whole slide scanning can be effectively normalized with the use of the color calibration slide.
      Citation: Journal of Pathology Informatics 2014 5(1):4-4
      PubDate: Fri,31 Jan 2014
      DOI: 10.4103/2153-3539.126153
      Issue No: Vol. 5, No. 1 (2014)
       
  • Intra-observer reproducibility of whole slide imaging for the primary
           diagnosis of breast needle biopsies
    • Authors: Carolina Reyes, Offiong F Ikpatt, Mehrdad Nadji, Richard J Cote
      Pages: 5 - 5
      Abstract: Carolina Reyes, Offiong F Ikpatt, Mehrdad Nadji, Richard J Cote

      Journal of Pathology Informatics 2014 5(1):5-5

      Background: Automated whole slide imaging (WSI), also known as virtual microscopy is rapidly becoming an important tool in diagnostic pathology. Currently, the primary utilization of the technique is for transmission of digital images, for second opinion consultation, as well as for quality assurance and education. The high-resolution of digital images along with the refinement of technology could now allow for WSI to be used as an alternative to conventional microscopy (CM) as a first line diagnostic platform. However, the accuracy and reproducibility of the technology for the routine histopathologic diagnosis has not been established yet. This study was undertaken to compare the intra-observer variability of WSI and CM in the primary diagnosis of breast biopsies. Materials and Methods: One hundred and three consecutive core needle biopsies of breast were selected for this study. Each slide was digitally scanned and the images were stored in a shared file. Three board-certified pathologists independently reviewed the glass slides by CM first, and in an interval of 2-3 weeks for the 2nd time to establish their baseline CM versus CM reproducibility. They then reviewed the digital images of all cases following the same interval of time to compare the reproducibility of WSI versus CM for each observer. The diagnostic categories included the typical range of benign and malignant mammary lesions. Results: The intra-observer variability for CM versus CM was 4%, 7%, and 0% for observers 1, 2, and 3 respectively. The diagnostic variability for WSI versus CM was 1%, 4%, and 1% for the same observers. All diagnostic disagreements were between ductal hyperplasia and atypical ductal hyperplasia. There was no intra-observer disagreement in the diagnosis of benign versus malignant disease. Conclusions: The intra-observer variability in the diagnosis of the core needle biopsies of the breast by high-resolution, WSI was the same as conventional glass slide microscopy. These results suggest that, WSI could be used similar to CM for the initial diagnosis of breast biopsies.
      Citation: Journal of Pathology Informatics 2014 5(1):5-5
      PubDate: Tue,25 Feb 2014
      DOI: 10.4103/2153-3539.127814
      Issue No: Vol. 5, No. 1 (2014)
       
  • Utility of alert-based CDSS in CPOE to improve compliance with plasma
           transfusion guidelines
    • Authors: Richard C Friedberg
      Pages: 6 - 6
      Abstract: Richard C Friedberg

      Journal of Pathology Informatics 2014 5(1):6-6


      Citation: Journal of Pathology Informatics 2014 5(1):6-6
      PubDate: Tue,25 Feb 2014
      Issue No: Vol. 5, No. 1 (2014)
       
  • The laboratory information system functionality assessment tool: Ensuring
           optimal software support for your laboratory
    • Authors: J Mark Tuthill, Bruce A Friedman, Ulysses J Balis, Andrew Splitz
      Pages: 7 - 7
      Abstract: J Mark Tuthill, Bruce A Friedman, Ulysses J Balis, Andrew Splitz

      Journal of Pathology Informatics 2014 5(1):7-7


      Citation: Journal of Pathology Informatics 2014 5(1):7-7
      PubDate: Tue,25 Feb 2014
      DOI: 10.4103/2153-3539.127819
      Issue No: Vol. 5, No. 1 (2014)
       
  • Histostitcher&#8482;: An informatics software platform for
           reconstructing whole-mount prostate histology using the extensible imaging
           platform framework
    • Authors: Robert J Toth, Natalie Shih, John E Tomaszewski, Michael D Feldman, Oliver Kutter, Daphne N Yu, John C Paulus, Ginaluca Paladini, Anant Madabhushi
      Pages: 8 - 8
      Abstract: Robert J Toth, Natalie Shih, John E Tomaszewski, Michael D Feldman, Oliver Kutter, Daphne N Yu, John C Paulus, Ginaluca Paladini, Anant Madabhushi

      Journal of Pathology Informatics 2014 5(1):8-8

      Context: Co-registration of ex-vivo histologic images with pre-operative imaging (e.g., magnetic resonance imaging [MRI]) can be used to align and map disease extent, and to identify quantitative imaging signatures. However, ex-vivo histology images are frequently sectioned into quarters prior to imaging. Aims: This work presents Histostitcher&#8482;, a software system designed to create a pseudo whole mount histology section (WMHS) from a stitching of four individual histology quadrant images. Materials and Methods: Histostitcher&#8482; uses user-identified fiducials on the boundary of two quadrants to stitch such quadrants. An original prototype of Histostitcher&#8482; was designed using the Matlab programming languages. However, clinical use was limited due to slow performance, computer memory constraints and an inefficient workflow. The latest version was created using the extensible imaging platform (XIP&#8482;) architecture in the C++ programming language. A fast, graphics processor unit renderer was designed to intelligently cache the visible parts of the histology quadrants and the workflow was significantly improved to allow modifying existing fiducials, fast transformations of the quadrants and saving/loading sessions. Results: The new stitching platform yielded significantly more efficient workflow and reconstruction than the previous prototype. It was tested on a traditional desktop computer, a Windows 8 Surface Pro table device and a 27 inch multi-touch display, with little performance difference between the different devices. Conclusions: Histostitcher&#8482; is a fast, efficient framework for reconstructing pseudo WMHS from individually imaged quadrants. The highly modular XIP&#8482; framework was used to develop an intuitive interface and future work will entail mapping the disease extent from the pseudo WMHS onto pre-operative MRI.
      Citation: Journal of Pathology Informatics 2014 5(1):8-8
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129441
      Issue No: Vol. 5, No. 1 (2014)
       
  • Peripheral blood smear image analysis: A comprehensive review
    • Authors: Emad A Mohammed, Mostafa M. A. Mohamed, Behrouz H Far, Christopher Naugler
      Pages: 9 - 9
      Abstract: Emad A Mohammed, Mostafa M. A. Mohamed, Behrouz H Far, Christopher Naugler

      Journal of Pathology Informatics 2014 5(1):9-9

      Peripheral blood smear image examination is a part of the routine work of every laboratory. The manual examination of these images is tedious, time-consuming and suffers from interobserver variation. This has motivated researchers to develop different algorithms and methods to automate peripheral blood smear image analysis. Image analysis itself consists of a sequence of steps consisting of image segmentation, features extraction and selection and pattern classification. The image segmentation step addresses the problem of extraction of the object or region of interest from the complicated peripheral blood smear image. Support vector machine (SVM) and artificial neural networks (ANNs) are two common approaches to image segmentation. Features extraction and selection aims to derive descriptive characteristics of the extracted object, which are similar within the same object class and different between different objects. This will facilitate the last step of the image analysis process: pattern classification. The goal of pattern classification is to assign a class to the selected features from a group of known classes. There are two types of classifier learning algorithms: supervised and unsupervised. Supervised learning algorithms predict the class of the object under test using training data of known classes. The training data have a predefined label for every class and the learning algorithm can utilize this data to predict the class of a test object. Unsupervised learning algorithms use unlabeled training data and divide them into groups using similarity measurements. Unsupervised learning algorithms predict the group to which a new test object belong to, based on the training data without giving an explicit class to that object. ANN, SVM, decision tree and K-nearest neighbor are possible approaches to classification algorithms. Increased discrimination may be obtained by combining several classifiers together.
      Citation: Journal of Pathology Informatics 2014 5(1):9-9
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129442
      Issue No: Vol. 5, No. 1 (2014)
       
  • Pocket pathologist: A mobile application for rapid diagnostic surgical
           pathology consultation
    • Authors: Douglas J Hartman, Anil V Parwani, Bill Cable, Ioan C Cucoranu, Jeff S McHugh, Brian J Kolowitz, Samuel A Yousem, Vijaykumar Palat, Anna Von Reden, Stephen Sloka, Gonzalo Romero Lauro, Ishtiaque Ahmed, Liron Pantanowitz
      Pages: 10 - 10
      Abstract: Douglas J Hartman, Anil V Parwani, Bill Cable, Ioan C Cucoranu, Jeff S McHugh, Brian J Kolowitz, Samuel A Yousem, Vijaykumar Palat, Anna Von Reden, Stephen Sloka, Gonzalo Romero Lauro, Ishtiaque Ahmed, Liron Pantanowitz

      Journal of Pathology Informatics 2014 5(1):10-10

      Introduction: Telepathology allows the digital transmission of images for rapid access to pathology experts. Recent technologic advances in smartphones have allowed them to be used to acquire and transmit digital images of the glass slide, representing cost savings and efficiency gains over traditional forms of telepathology. We report our experience with developing an iPhone application (App - Pocket Pathologist) to facilitate rapid diagnostic pathology teleconsultation utilizing a smartphone. Materials and Methods: A secure, web-based portal (http://pathconsult.upmc.com/) was created to facilitate remote transmission of digital images for teleconsultation. The App augments functionality of the web-based portal and allows the user to quickly and easily upload digital images for teleconsultation. Image quality of smartphone cameras was evaluated by capturing images using different adapters that directly attach phones to a microscope ocular lens. Results: The App was launched in August 2013. The App facilitated easy submission of cases for teleconsultation by limiting the number of data entry fields for users and enabling uploading of images from their smartphone's gallery wirelessly. Smartphone cameras properly attached to a microscope create static digital images of similar quality to a commercial digital microscope camera. Conclusion: Smartphones have great potential to support telepathology because they are portable, provide ubiquitous internet connectivity, contain excellent digital cameras, and can be easily attached to a microscope. The Pocket Pathologist App represents a significant reduction in the cost of creating digital images and submitting them for teleconsultation. The iPhone App provides an easy solution for global users to submit digital pathology images to pathology experts for consultation.
      Citation: Journal of Pathology Informatics 2014 5(1):10-10
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129443
      Issue No: Vol. 5, No. 1 (2014)
       
  • Pathology informatics fellowship training: Focus on molecular pathology
    • Authors: Diana Mandelker, Roy E Lee, Mia Y Platt, Gregory Riedlinger, Andrew Quinn, Luigi K. F. Rao, Veronica E Klepeis, Michael Mahowald, William J Lane, Bruce A Beckwith, Jason M Baron, David S McClintock, Frank C Kuo, Matthew S Lebo, John R Gilbertson
      Pages: 11 - 11
      Abstract: Diana Mandelker, Roy E Lee, Mia Y Platt, Gregory Riedlinger, Andrew Quinn, Luigi K. F. Rao, Veronica E Klepeis, Michael Mahowald, William J Lane, Bruce A Beckwith, Jason M Baron, David S McClintock, Frank C Kuo, Matthew S Lebo, John R Gilbertson

      Journal of Pathology Informatics 2014 5(1):11-11

      Background: Pathology informatics is both emerging as a distinct subspecialty and simultaneously becoming deeply integrated within the breadth of pathology practice. As specialists, pathology informaticians need a broad skill set, including aptitude with information fundamentals, information systems, workflow and process, and governance and management. Currently, many of those seeking training in pathology informatics additionally choose training in a second subspecialty. Combining pathology informatics training with molecular pathology is a natural extension, as molecular pathology is a subspecialty with high potential for application of modern biomedical informatics techniques. Methods and Results: Pathology informatics and molecular pathology fellows and faculty evaluated the current fellowship program's core curriculum topics and subtopics for relevance to molecular pathology. By focusing on the overlap between the two disciplines, a structured curriculum consisting of didactics, operational rotations, and research projects was developed for those fellows interested in both pathology informatics and molecular pathology. Conclusions: The scope of molecular diagnostics is expanding dramatically as technology advances and our understanding of disease extends to the genetic level. Here, we highlight many of the informatics challenges facing molecular pathology today, and outline specific informatics principles necessary for the training of future molecular pathologists.
      Citation: Journal of Pathology Informatics 2014 5(1):11-11
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129444
      Issue No: Vol. 5, No. 1 (2014)
       
  • Autoverification in a core clinical chemistry laboratory at an academic
           medical center
    • Authors: Matthew D Krasowski, Scott R Davis, Denny Drees, Cory Morris, Jeff Kulhavy, Cheri Crone, Tami Bebber, Iwa Clark, David L Nelson, Sharon Teul, Dena Voss, Dean Aman, Julie Fahnle, John L Blau
      Pages: 13 - 13
      Abstract: Matthew D Krasowski, Scott R Davis, Denny Drees, Cory Morris, Jeff Kulhavy, Cheri Crone, Tami Bebber, Iwa Clark, David L Nelson, Sharon Teul, Dena Voss, Dean Aman, Julie Fahnle, John L Blau

      Journal of Pathology Informatics 2014 5(1):13-13

      Background: Autoverification is a process of using computer-based rules to verify clinical laboratory test results without manual intervention. To date, there is little published data on the use of autoverification over the course of years in a clinical laboratory. We describe the evolution and application of autoverification in an academic medical center clinical chemistry core laboratory. Subjects and Methods: At the institution of the study, autoverification developed from rudimentary rules in the laboratory information system (LIS) to extensive and sophisticated rules mostly in middleware software. Rules incorporated decisions based on instrument error flags, interference indices, analytical measurement ranges (AMRs), delta checks, dilution protocols, results suggestive of compromised or contaminated specimens, and 'absurd' (physiologically improbable) values. Results: The autoverification rate for tests performed in the core clinical chemistry laboratory has increased over the course of 13 years from 40% to the current overall rate of 99.5%. A high percentage of critical values now autoverify. The highest rates of autoverification occurred with the most frequently ordered tests such as the basic metabolic panel (sodium, potassium, chloride, carbon dioxide, creatinine, blood urea nitrogen, calcium, glucose; 99.6%), albumin (99.8%), and alanine aminotransferase (99.7%). The lowest rates of autoverification occurred with some therapeutic drug levels (gentamicin, lithium, and methotrexate) and with serum free light chains (kappa/lambda), mostly due to need for offline dilution and manual filing of results. Rules also caught very rare occurrences such as plasma albumin exceeding total protein (usually indicative of an error such as short sample or bubble that evaded detection) and marked discrepancy between total bilirubin and the spectrophotometric icteric index (usually due to interference of the bilirubin assay by immunoglobulin (Ig) M monoclonal gammopathy). Conclusions: Our results suggest that a high rate of autoverification is possible with modern clinical chemistry analyzers. The ability to autoverify a high percentage of results increases productivity and allows clinical laboratory staff to focus attention on the small number of specimens and results that require manual review and investigation.
      Citation: Journal of Pathology Informatics 2014 5(1):13-13
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129450
      Issue No: Vol. 5, No. 1 (2014)
       
  • Implementation of large-scale routine diagnostics using whole slide
           imaging in Sweden: Digital pathology experiences 2006-2013
    • Authors: Sten Thorstenson, Jesper Molin, Claes Lundström
      Pages: 14 - 14
      Abstract: Sten Thorstenson, Jesper Molin, Claes Lundström

      Journal of Pathology Informatics 2014 5(1):14-14

      Recent technological advances have improved the whole slide imaging (WSI) scanner quality and reduced the cost of storage, thereby enabling the deployment of digital pathology for routine diagnostics. In this paper we present the experiences from two Swedish sites having deployed routine large-scale WSI for primary review. At Kalmar County Hospital, the digitization process started in 2006 to reduce the time spent at the microscope in order to improve the ergonomics. Since 2008, more than 500,000 glass slides have been scanned in the routine operations of Kalmar and the neighboring Link&#246;ping University Hospital. All glass slides are digitally scanned yet they are also physically delivered to the consulting pathologist who can choose to review the slides on screen, in the microscope, or both. The digital operations include regular remote case reporting by a few hospital pathologists, as well as around 150 cases per week where primary review is outsourced to a private clinic. To investigate how the pathologists choose to use the digital slides, a web-based questionnaire was designed and sent out to the pathologists in Kalmar and Link&#246;ping. The responses showed that almost all pathologists think that ergonomics have improved and that image quality was sufficient for most histopathologic diagnostic work. 38 &#177; 28% of the cases were diagnosed digitally, but the survey also revealed that the pathologists commonly switch back and forth between digital and conventional microscopy within the same case. The fact that two full-scale digital systems have been implemented and that a large portion of the primary reporting is voluntarily performed digitally shows that large-scale digitization is possible today.
      Citation: Journal of Pathology Informatics 2014 5(1):14-14
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129452
      Issue No: Vol. 5, No. 1 (2014)
       
  • Guidelines from the Canadian Association of Pathologists for establishing
           a telepathology service for anatomic pathology using whole-slide imaging
    • Authors: Chantal Bernard, SA Chandrakanth, Ian Scott Cornell, James Dalton, Andrew Evans, Bertha M Garcia, Chris Godin, Marek Godlewski, Gerard H Jansen, Amin Kabani, Said Louahlia, Lisa Manning, Raymond Maung, Lisa Moore, Joanne Philley, Jack Slatnik, John Srigley, Alain Thibault, Donald Daniel Picard, Hanah Cracower, Bernard Tetu
      Pages: 15 - 15
      Abstract: Chantal Bernard, SA Chandrakanth, Ian Scott Cornell, James Dalton, Andrew Evans, Bertha M Garcia, Chris Godin, Marek Godlewski, Gerard H Jansen, Amin Kabani, Said Louahlia, Lisa Manning, Raymond Maung, Lisa Moore, Joanne Philley, Jack Slatnik, John Srigley, Alain Thibault, Donald Daniel Picard, Hanah Cracower, Bernard Tetu

      Journal of Pathology Informatics 2014 5(1):15-15

      The use of telepathology for clinical applications in Canada has steadily become more attractive over the last 10 years, driven largely by its potential to provide rapid pathology consulting services throughout the country regardless of the location of a particular institution. Based on this trend, the president of the Canadian Association of Pathologists asked a working group consisting of pathologists, technologists, and healthcare administrators from across Canada to oversee the development of guidelines to provide Canadian pathologists with basic information on how to implement and use this technology. The guidelines were systematically developed, based on available medical literature and the clinical experience of early adopters of telepathology in Canada. While there are many different modalities and applications of telepathology, this document focuses specifically on whole-slide imaging as applied to intraoperative pathology consultation (frozen section), primary diagnosis, expert or second opinions and quality assurance activities. Applications such as hematopathology, microbiology, tumour boards, education, research and technical and/or standard-related issues are not covered.
      Citation: Journal of Pathology Informatics 2014 5(1):15-15
      PubDate: Fri,28 Mar 2014
      DOI: 10.4103/2153-3539.129455
      Issue No: Vol. 5, No. 1 (2014)
       
  • HyMaP: A hybrid magnitude-phase approach to unsupervised segmentation of
           tumor areas in breast cancer histology images
    • Authors: Adnan M Khan, Hesham El-Daly, Emma Simmons, Nasir M Rajpoot
      Pages: 1 - 1
      Abstract: Adnan M Khan, Hesham El-Daly, Emma Simmons, Nasir M Rajpoot

      Journal of Pathology Informatics 2013 4(2):1-1

      Background: Segmentation of areas containing tumor cells in standard H&E histopathology images of breast (and several other tissues) is a key task for computer-assisted assessment and grading of histopathology slides. Good segmentation of tumor regions is also vital for automated scoring of immunohistochemical stained slides to restrict the scoring or analysis to areas containing tumor cells only and avoid potentially misleading results from analysis of stromal regions. Furthermore, detection of mitotic cells is critical for calculating key measures such as mitotic index; a key criteria for grading several types of cancers including breast cancer. We show that tumor segmentation can allow detection and quantification of mitotic cells from the standard H&E slides with a high degree of accuracy without need for special stains, in turn making the whole process more cost-effective. Method: Based on the tissue morphology, breast histology image contents can be divided into four regions: Tumor, Hypocellular Stroma (HypoCS), Hypercellular Stroma (HyperCS), and tissue fat (Background). Background is removed during the preprocessing stage on the basis of color thresholding, while HypoCS and HyperCS regions are segmented by calculating features using magnitude and phase spectra in the frequency domain, respectively, and performing unsupervised segmentation on these features. Results: All images in the database were hand segmented by two expert pathologists. The algorithms considered here are evaluated on three pixel-wise accuracy measures: precision, recall, and F1-Score. The segmentation results obtained by combining HypoCS and HyperCS yield high F1-Score of 0.86 and 0.89 with re-spect to the ground truth. Conclusions: In this paper, we show that segmentation of breast histopathology image into hypocellular stroma and hypercellular stroma can be achieved using magnitude and phase spectra in the frequency domain. The segmentation leads to demarcation of tumor margins leading to improved accuracy of mitotic cell detection.
      Citation: Journal of Pathology Informatics 2013 4(2):1-1
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109802
      Issue No: Vol. 4, No. 2 (2013)
       
  • TMARKER: A free software toolkit for histopathological cell counting and
           staining estimation
    • Authors: Peter J Schüffler, Thomas J Fuchs, Cheng Soon Ong, Peter J Wild, Niels J Rupp, Joachim M Buhmann
      Pages: 2 - 2
      Abstract: Peter J Schüffler, Thomas J Fuchs, Cheng Soon Ong, Peter J Wild, Niels J Rupp, Joachim M Buhmann

      Journal of Pathology Informatics 2013 4(2):2-2

      Background: Histological tissue analysis often involves manual cell counting and staining estimation of cancerous cells. These assessments are extremely time consuming, highly subjective and prone to error, since immunohistochemically stained cancer tissues usually show high variability in cell sizes, morphological structures and staining quality. To facilitate reproducible analysis in clinical practice as well as for cancer research, objective computer assisted staining estimation is highly desirable. Methods: We employ machine learning algorithms as randomized decision trees and support vector machines for nucleus detection and classification. Superpixels as segmentation over the tissue image are classified into foreground and background and thereafter into malignant and benign, learning from the user's feedback. As a fast alternative without nucleus classification, the existing color deconvolution method is incorporated. Results: Our program TMARKER connects already available workflows for computational pathology and immunohistochemical tissue rating with modern active learning algorithms from machine learning and computer vision. On a test dataset of human renal clear cell carcinoma and prostate carcinoma, the performance of the used algorithms is equivalent to two independent pathologists for nucleus detection and classification. Conclusion: We present a novel, free and operating system independent software package for computational cell counting and staining estimation, supporting IHC stained tissue analysis in clinic and for research. Proprietary toolboxes for similar tasks are expensive, bound to specific commercial hardware (e.g. a microscope) and mostly not quantitatively validated in terms of performance and reproducibility. We are confident that the presented software package will proof valuable for the scientific community and we anticipate a broader application domain due to the possibility to interactively learn models for new image types.
      Citation: Journal of Pathology Informatics 2013 4(2):2-2
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109804
      Issue No: Vol. 4, No. 2 (2013)
       
  • Automated segmentation of atherosclerotic histology based on pattern
           classification
    • Authors: Arna van Engelen, Wiro J Niessen, Stefan Klein, Harald C Groen, Kim van Gaalen, Hence J Verhagen, Jolanda J Wentzel, Aad van der Lugt, Marleen de Bruijne
      Pages: 3 - 3
      Abstract: Arna van Engelen, Wiro J Niessen, Stefan Klein, Harald C Groen, Kim van Gaalen, Hence J Verhagen, Jolanda J Wentzel, Aad van der Lugt, Marleen de Bruijne

      Journal of Pathology Informatics 2013 4(2):3-3

      Background: Histology sections provide accurate information on atherosclerotic plaque composition, and are used in various applications. To our knowledge, no automated systems for plaque component segmentation in histology sections currently exist. Materials and Methods: We perform pixel-wise classification of fibrous, lipid, and necrotic tissue in Elastica Von Gieson-stained histology sections, using features based on color channel intensity and local image texture and structure. We compare an approach where we train on independent data to an approach where we train on one or two sections per specimen in order to segment the remaining sections. We evaluate the results on segmentation accuracy in histology, and we use the obtained histology segmentations to train plaque component classification methods in ex vivo Magnetic resonance imaging (MRI) and in vivo MRI and computed tomography (CT). Results: In leave-one-specimen-out experiments on 176 histology slices of 13 plaques, a pixel-wise accuracy of 75.7 &#177; 6.8% was obtained. This increased to 77.6 &#177; 6.5% when two manually annotated slices of the specimen to be segmented were used for training. Rank correlations of relative component volumes with manually annotated volumes were high in this situation (P = 0.82-0.98). Using the obtained histology segmentations to train plaque component classification methods in ex vivo MRI and in vivo MRI and CT resulted in similar image segmentations for training on the automated histology segmentations as for training on a fully manual ground truth. The size of the lipid-rich necrotic core was significantly smaller when training on fully automated histology segmentations than when manually annotated histology sections were used. This difference was reduced and not statistically significant when one or two slices per section were manually annotated for histology segmentation. Conclusions: Good histology segmentations can be obtained by automated segmentation, which show good correlations with ground truth volumes. In addition, these can be used to develop segmentation methods in other imaging modalities. Accuracy increases when one or two sections of the same specimen are used for training, which requires a limited amount of user interaction in practice.
      Citation: Journal of Pathology Informatics 2013 4(2):3-3
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109844
      Issue No: Vol. 4, No. 2 (2013)
       
  • A statistical framework for analyzing hypothesized interactions between
           cells imaged using multispectral microscopy and multiple
           immunohistochemical markers
    • Authors: Chris J Rose, Khimara Naidoo, Vanessa Clay, Kim Linton, John A Radford, Richard J Byers
      Pages: 4 - 4
      Abstract: Chris J Rose, Khimara Naidoo, Vanessa Clay, Kim Linton, John A Radford, Richard J Byers

      Journal of Pathology Informatics 2013 4(2):4-4

      Background: Multispectral microscopy and multiple staining can be used to identify cells with distinct immunohistochemical (IHC) characteristics. We present here a method called hypothesized interaction distribution (HID) analysis for characterizing the statistical distribution of pair-wise spatial relationships between cells with particular IHC characteristics and apply it to clinical data. Materials and Methods: We retrospectively analyzed data from a study of 26 follicular lymphoma patients in which sections were stained for CD20 and YY1. HID analysis, using leave-one-out validation, was used to assign patients to one of two groups. We tested the null hypothesis of no difference in Kaplan-Meier survival curves between the groups. Results: Shannon entropy of HIDs assigned patients to groups that had significantly different survival curves (median survival was 7.70 versus 110 months, P = 0.00750). Hypothesized interactions between pairs of cells positive for both CD20 and YY1 were associated with poor survival. Conclusions: HID analysis provides quantitative inferences about possible interactions between spatially proximal cells with particular IHC characteristics. In follicular lymphoma, HID analysis was able to distinguish between patients with poor versus good survival, and it may have diagnostic and prognostic utility in this and other diseases.
      Citation: Journal of Pathology Informatics 2013 4(2):4-4
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109856
      Issue No: Vol. 4, No. 2 (2013)
       
  • Approaches to automatic parameter fitting in a microscopy image
           segmentation pipeline: An exploratory parameter space analysis
    • Authors: Christian Held, Tim Nattkemper, Ralf Palmisano, Thomas Wittenberg
      Pages: 5 - 5
      Abstract: Christian Held, Tim Nattkemper, Ralf Palmisano, Thomas Wittenberg

      Journal of Pathology Informatics 2013 4(2):5-5

      Introduction: Research and diagnosis in medicine and biology often require the assessment of a large amount of microscopy image data. Although on the one hand, digital pathology and new bioimaging technologies find their way into clinical practice and pharmaceutical research, some general methodological issues in automated image analysis are still open. Methods: In this study, we address the problem of fitting the parameters in a microscopy image segmentation pipeline. We propose to fit the parameters of the pipeline's modules with optimization algorithms, such as, genetic algorithms or coordinate descents, and show how visual exploration of the parameter space can help to identify sub-optimal parameter settings that need to be avoided. Results: This is of significant help in the design of our automatic parameter fitting framework, which enables us to tune the pipeline for large sets of micrographs. Conclusion: The underlying parameter spaces pose a challenge for manual as well as automated parameter optimization, as the parameter spaces can show several local performance maxima. Hence, optimization strategies that are not able to jump out of local performance maxima, like the hill climbing algorithm, often result in a local maximum.
      Citation: Journal of Pathology Informatics 2013 4(2):5-5
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109831
      Issue No: Vol. 4, No. 2 (2013)
       
  • Stain guided mean-shift filtering in automatic detection of human tissue
           nuclei
    • Authors: Yu Zhou, Derek Magee, Darren Treanor, Andrew Bulpitt
      Pages: 6 - 6
      Abstract: Yu Zhou, Derek Magee, Darren Treanor, Andrew Bulpitt

      Journal of Pathology Informatics 2013 4(2):6-6

      Background: As a critical technique in a digital pathology laboratory, automatic nuclear detection has been investigated for more than one decade. Conventional methods work on the raw images directly whose color/intensity homogeneity within tissue/cell areas are undermined due to artefacts such as uneven staining, making the subsequent binarization process prone to error. This paper concerns detecting cell nuclei automatically from digital pathology images by enhancing the color homogeneity as a pre-processing step. Methods: Unlike previous watershed based algorithms relying on post-processing of the watershed, we present a new method that incorporates the staining information of pathological slides in the analysis. This pre-processing step strengthens the color homogeneity within the nuclear areas as well as the background areas, while keeping the nuclear edges sharp. Proof of convergence for the proposed algorithm is also provided. After pre-processing, Otsu's threshold is applied to binarize the image, which is further segmented via watershed. To keep a proper compromise between removing overlapping and avoiding over-segmentation, a naive Bayes classifier is designed to refine the splits suggested by the watershed segmentation. Results: The method is validated with 10 sets of 1000 &#215; 1000 pathology images of lymphoma from one digital slide. The mean precision and recall rates are 87% and 91%, corresponding to a mean F-score equal to 89%. Standard deviations for these performance indicators are 5.1%, 1.6% and 3.2% respectively. Conclusion: The precision/recall performance obtained indicates that the proposed method outperforms several other alternatives. In particular, for nuclear detection, stain guided mean-shift (SGMS) is more effective than the direct application of mean-shift in pre-processing. Our experiments also show that pre-processing the digital pathology images with SGMS gives better results than conventional watershed algorithms. Nevertheless, as only one type of tissue is tested in this paper, a further study is planned to enhance the robustness of the algorithm so that other types of tissues/stains can also be processed reliably.
      Citation: Journal of Pathology Informatics 2013 4(2):6-6
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109863
      Issue No: Vol. 4, No. 2 (2013)
       
  • 3D reconstruction of multiple stained histology images
    • Authors: Yi Song, Darren Treanor, Andrew J Bulpitt, Derek R Magee
      Pages: 7 - 7
      Abstract: Yi Song, Darren Treanor, Andrew J Bulpitt, Derek R Magee

      Journal of Pathology Informatics 2013 4(2):7-7

      Context: Three dimensional (3D) tissue reconstructions from the histology images with different stains allows the spatial alignment of structural and functional elements highlighted by different stains for quantitative study of many physiological and pathological phenomena. This has significant potential to improve the understanding of the growth patterns and the spatial arrangement of diseased cells, and enhance the study of biomechanical behavior of the tissue structures towards better treatments (e.g. tissue-engineering applications). Methods: This paper evaluates three strategies for 3D reconstruction from sets of two dimensional (2D) histological sections with different stains, by combining methods of 2D multi-stain registration and 3D volumetric reconstruction from same stain sections. Setting and Design: The different strategies have been evaluated on two liver specimens (80 sections in total) stained with Hematoxylin and Eosin (H and E), Sirius Red, and Cytokeratin (CK) 7. Results and Conclusion: A strategy of using multi-stain registration to align images of a second stain to a volume reconstructed by same-stain registration results in the lowest overall error, although an interlaced image registration approach may be more robust to poor section quality.
      Citation: Journal of Pathology Informatics 2013 4(2):7-7
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109864
      Issue No: Vol. 4, No. 2 (2013)
       
  • Quantifying local heterogeneity via morphologic scale: Distinguishing
           tumoral from stromal regions
    • Authors: Andrew Janowczyk, Sharat Chandran, Anant Madabhushi
      Pages: 8 - 8
      Abstract: Andrew Janowczyk, Sharat Chandran, Anant Madabhushi

      Journal of Pathology Informatics 2013 4(2):8-8

      Introduction: The notion of local scale was introduced to characterize varying levels of image detail so that localized image processing tasks could be performed while simultaneously yielding a globally optimal result. In this paper, we have presented the methodological framework for a novel locally adaptive scale definition, morphologic scale (MS), which is different from extant local scale definitions in that it attempts to characterize local heterogeneity as opposed to local homogeneity. Methods: At every point of interest, the MS is determined as a series of radial paths extending outward in the direction of least resistance, navigating around obstructions. Each pixel can then be directly compared to other points of interest via a rotationally invariant quantitative feature descriptor, determined by the application of Fourier descriptors to the collection of these paths. Results: Our goal is to distinguish tumor and stromal tissue classes in the context of four different digitized pathology datasets: prostate tissue microarrays (TMAs) stained with hematoxylin and eosin (HE) (44 images) and TMAs stained with only hematoxylin (H) (44 images), slide mounts of ovarian H (60 images), and HE breast cancer (51 images) histology images. Classification performance over 50 cross-validation runs using a Bayesian classifier produced mean areas under the curve of 0.88 &#177; 0.01 (prostate HE), 0.87 &#177; 0.02 (prostate H), 0.88 &#177; 0.01 (ovarian H), and 0.80 &#177; 0.01 (breast HE). Conclusion: For each dataset listed in [Table 3], we randomly selected 100 points per image, and using the procedure described in Experiment 1, we attempted to separate them as belonging to stroma or epithelium.
      Citation: Journal of Pathology Informatics 2013 4(2):8-8
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109865
      Issue No: Vol. 4, No. 2 (2013)
       
  • Real-time whole slide mosaicing for non-automated microscopes in
           histopathology analysis
    • Authors: Alessandro Gherardi, Alessandro Bevilacqua
      Pages: 9 - 9
      Abstract: Alessandro Gherardi, Alessandro Bevilacqua

      Journal of Pathology Informatics 2013 4(2):9-9

      Context: Mosaics of Whole Slides (WS) are a valuable resource for pathologists to have the whole sample available at high resolution. The WS mosaic provides pathologists with an overview of the whole sample at a glance, helping them to make a reliable diagnosis. Despite recent solutions exist for creating WS mosaics based, for instance, on automated microscopes with motorized stages or WS scanner, most of the histopathology analysis are still performed in laboratories endowed with standard manual stage microscopes. Nowadays, there are lots of dedicated devices and hardware to achieve WS automatically and in batch, but only few of them are conceived to work tightly connected with a microscope and none of them is capable of working in real-time with common light microscopes. However, there is a need of having low-cost yet effective mosaicing applications even in small laboratories to improve routine histopathological analyses or to perform remote diagnoses. Aims: The purpose of this work is to study and develop a real-time mosaicing algorithm working even using non-automated microscopes, to enable pathologists to achieve WS while moving the holder manually, without exploiting any dedicated device. This choice enables pathologists to build WS in real-time, while browsing the sample as they are accustomed to, helping them to identify, locate, and digitally annotate lesions fast. Materials and Methods: Our method exploits fast feature tracker and frame to frame registration that we implemented on common graphics processing unit cards. The system work with common light microscopes endowed with a digital camera and connected to a commodity personal computer. Result and Conclusion: The system has been tested on several histological samples to test the effectiveness of the algorithm to work with mosaicing having different appearances as far as brightness, contrast, texture, and detail levels are concerned, attaining sub-pixel registration accuracy at real-time interactive rates.
      Citation: Journal of Pathology Informatics 2013 4(2):9-9
      PubDate: Sat,30 Mar 2013
      Issue No: Vol. 4, No. 2 (2013)
       
  • Registration of histological whole slide images guided by vessel
           structures
    • Authors: Michael Schwier, Tobias Böhler, Horst Karl Hahn, Uta Dahmen, Olaf Dirsch
      Pages: 10 - 10
      Abstract: Michael Schwier, Tobias Böhler, Horst Karl Hahn, Uta Dahmen, Olaf Dirsch

      Journal of Pathology Informatics 2013 4(2):10-10

      Introduction: The registration of histological whole slide images is an important prerequisite for modern histological image analysis. A partial reconstruction of the original volume allows e.g. colocalization analysis of tissue parameters or high-detail reconstructions of anatomical structures in 3D. Methods: In this paper, we present an automatic staining-invariant registration method, and as part of that, introduce a novel vessel-based rigid registration algorithm using a custom similarity measure. The method is based on an iterative best-fit matching of prominent vessel structures. Results: We evaluated our method on a sophisticated synthetic dataset as well as on real histological whole slide images. Based on labeled vessel structures we compared the relative differences for corresponding structures. The average positional error was close to 0, the median for the size change factor was 1, and the median overlap was 0.77. Conclusion: The results show that our approach is very robust and creates high quality reconstructions. The key element for the resulting quality is our novel rigid registration algorithm.
      Citation: Journal of Pathology Informatics 2013 4(2):10-10
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109868
      Issue No: Vol. 4, No. 2 (2013)
       
  • Histological stain evaluation for machine learning applications
    • Authors: Jimmy C Azar, Christer Busch, Ingrid B Carlbom
      Pages: 11 - 11
      Abstract: Jimmy C Azar, Christer Busch, Ingrid B Carlbom

      Journal of Pathology Informatics 2013 4(2):11-11

      Aims: A methodology for quantitative comparison of histological stains based on their classification and clustering performance, which may facilitate the choice of histological stains for automatic pattern and image analysis. Background: Machine learning and image analysis are becoming increasingly important in pathology applications for automatic analysis of histological tissue samples. Pathologists rely on multiple, contrasting stains to analyze tissue samples, but histological stains are developed for visual analysis and are not always ideal for automatic analysis. Materials and Methods: Thirteen different histological stains were used to stain adjacent prostate tissue sections from radical prostatectomies. We evaluate the stains for both supervised and unsupervised classification of stain/tissue combinations. For supervised classification we measure the error rate of nonlinear support vector machines, and for unsupervised classification we use the Rand index and the F-measure to assess the clustering results of a Gaussian mixture model based on expectation-maximization. Finally, we investigate class separability measures based on scatter criteria. Results: A methodology for quantitative evaluation of histological stains in terms of their classification and clustering efficacy that aims at improving segmentation and color decomposition. We demonstrate that for a specific tissue type, certain stains perform consistently better than others according to objective error criteria. Conclusions: The choice of histological stain for automatic analysis must be based on its classification and clustering performance, which are indicators of the performance of automatic segmentation of tissue into morphological components, which in turn may be the basis for diagnosis.
      Citation: Journal of Pathology Informatics 2013 4(2):11-11
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109869
      Issue No: Vol. 4, No. 2 (2013)
       
  • Automated mitosis detection using texture, SIFT features and HMAX
           biologically inspired approach
    • Authors: Humayun Irshad, Sepehr Jalali, Ludovic Roux, Daniel Racoceanu, Lim Joo Hwee, Gilles Le Naour, Frédérique Capron
      Pages: 12 - 12
      Abstract: Humayun Irshad, Sepehr Jalali, Ludovic Roux, Daniel Racoceanu, Lim Joo Hwee, Gilles Le Naour, Frédérique Capron

      Journal of Pathology Informatics 2013 4(2):12-12

      Context: According to Nottingham grading system, mitosis count in breast cancer histopathology is one of three components required for cancer grading and prognosis. Manual counting of mitosis is tedious and subject to considerable inter- and intra-reader variations. Aims: The aim is to investigate the various texture features and Hierarchical Model and X (HMAX) biologically inspired approach for mitosis detection using machine-learning techniques. Materials and Methods: We propose an approach that assists pathologists in automated mitosis detection and counting. The proposed method, which is based on the most favorable texture features combination, examines the separability between different channels of color space. Blue-ratio channel provides more discriminative information for mitosis detection in histopathological images. Co-occurrence features, run-length features, and Scale-invariant feature transform (SIFT) features were extracted and used in the classification of mitosis. Finally, a classification is performed to put the candidate patch either in the mitosis class or in the non-mitosis class. Three different classifiers have been evaluated: Decision tree, linear kernel Support Vector Machine (SVM), and non-linear kernel SVM. We also evaluate the performance of the proposed framework using the modified biologically inspired model of HMAX and compare the results with other feature extraction methods such as dense SIFT. Results: The proposed method has been tested on Mitosis detection in breast cancer histological images (MITOS) dataset provided for an International Conference on Pattern Recognition (ICPR) 2012 contest. The proposed framework achieved 76% recall, 75% precision and 76% F-measure. Conclusions: Different frameworks for classification have been evaluated for mitosis detection. In future work, instead of regions, we intend to compute features on the results of mitosis contour segmentation and use them to improve detection and classification rate.
      Citation: Journal of Pathology Informatics 2013 4(2):12-12
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109870
      Issue No: Vol. 4, No. 2 (2013)
       
  • Immunohistochemical analysis of breast tissue microarray images using
           contextual classifiers
    • Authors: Stephen J McKenna, Telmo Amaral, Shazia Akbar, Lee Jordan, Alastair Thompson
      Pages: 13 - 13
      Abstract: Stephen J McKenna, Telmo Amaral, Shazia Akbar, Lee Jordan, Alastair Thompson

      Journal of Pathology Informatics 2013 4(2):13-13

      Background: Tissue microarrays (TMAs) are an important tool in translational research for examining multiple cancers for molecular and protein markers. Automatic immunohistochemical (IHC) scoring of breast TMA images remains a challenging problem. Methods: A two-stage approach that involves localization of regions of invasive and in-situ carcinoma followed by ordinal IHC scoring of nuclei in these regions is proposed. The localization stage classifies locations on a grid as tumor or non-tumor based on local image features. These classifications are then refined using an auto-context algorithm called spin-context. Spin-context uses a series of classifiers to integrate image feature information with spatial context information in the form of estimated class probabilities. This is achieved in a rotationally-invariant manner. The second stage estimates ordinal IHC scores in terms of the strength of staining and the proportion of nuclei stained. These estimates take the form of posterior probabilities, enabling images with uncertain scores to be referred for pathologist review. Results: The method was validated against manual pathologist scoring on two nuclear markers, progesterone receptor (PR) and estrogen receptor (ER). Errors for PR data were consistently lower than those achieved with ER data. Scoring was in terms of estimated proportion of cells that were positively stained (scored on an ordinal scale of 0-6) and perceived strength of staining (scored on an ordinal scale of 0-3). Average absolute differences between predicted scores and pathologist-assigned scores were 0.74 for proportion of cells and 0.35 for strength of staining (PR). Conclusions: The use of context information via spin-context improved the precision and recall of tumor localization. The combination of the spin-context localization method with the automated scoring method resulted in reduced IHC scoring errors.
      Citation: Journal of Pathology Informatics 2013 4(2):13-13
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109871
      Issue No: Vol. 4, No. 2 (2013)
       
  • Automated classification of immunostaining patterns in breast tissue from
           the human protein Atlas
    • Authors: Issac Niwas Swamidoss, Andreas Kårsnäs, Virginie Uhlmann, Palanisamy Ponnusamy, Caroline Kampf, Martin Simonsson, Carolina Wählby, Robin Strand
      Pages: 14 - 14
      Abstract: Issac Niwas Swamidoss, Andreas Kårsnäs, Virginie Uhlmann, Palanisamy Ponnusamy, Caroline Kampf, Martin Simonsson, Carolina Wählby, Robin Strand

      Journal of Pathology Informatics 2013 4(2):14-14

      Background: The Human Protein Atlas (HPA) is an effort to map the location of all human proteins (http://www.proteinatlas.org/). It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA) are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. Materials and Methods: The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM) features, complex wavelet co-occurrence matrix (CWCM) features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM)-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM) and linear discriminant analysis (LDA) classifier). Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. Results: We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Conclusions: Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for quantification of staining patterns in histopathology have many applications, ranging from antibody quality control to tumor grading.
      Citation: Journal of Pathology Informatics 2013 4(2):14-14
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109881
      Issue No: Vol. 4, No. 2 (2013)
       
  • Scalable system for classification of white blood cells from Leishman
           stained blood stain images
    • Authors: Atin Mathur, Ardhendu S Tripathi, Manohar Kuse
      Pages: 15 - 15
      Abstract: Atin Mathur, Ardhendu S Tripathi, Manohar Kuse

      Journal of Pathology Informatics 2013 4(2):15-15

      Introduction: The White Blood Cell (WBC) differential count yields clinically relevant information about health and disease. Currently, pathologists manually annotate the WBCs, which is time consuming and susceptible to error, due to the tedious nature of the process. This study aims at automation of the Differential Blood Count (DBC) process, so as to increase productivity and eliminate human errors. Materials and Methods: The proposed system takes the peripheral Leishman blood stain images as the input and generates a count for each of the WBC subtypes. The digitized microscopic images are stain normalized for the segmentation, to be consistent over a diverse set of slide images. Active contours are employed for robust segmentation of the WBC nucleus and cytoplasm. The seed points are generated by processing the images in Hue-Saturation-Value (HSV) color space. An efficient method for computing a new feature, 'number of lobes,' for discrimination of WBC subtypes, is introduced in this article. This method is based on the concept of minimization of the compactness of each lobe. The Naive Bayes classifier, with Laplacian correction, provides a fast, efficient, and robust solution to multiclass categorization problems. This classifier is characterized by incremental learning and can also be embedded within the database systems. Results: An overall accuracy of 92.45% and 92.72% over the training and testing sets has been obtained, respectively. Conclusion: Thus, incremental learning is inducted into the Naive Bayes Classifier, to facilitate fast, robust, and efficient classification, which is evident from the high sensitivity achieved for all the subtypes of WBCs.
      Citation: Journal of Pathology Informatics 2013 4(2):15-15
      PubDate: Sat,30 Mar 2013
      DOI: 10.4103/2153-3539.109883
      Issue No: Vol. 4, No. 2 (2013)
       
  • The successful implementation of a licensed data management interface
           between a Sunquest&#174; laboratory information system and an AB
           SCIEX TM mass spectrometer
    • Authors: Deborah French, Enrique Terrazas
      Pages: 1 - 1
      Abstract: Deborah French, Enrique Terrazas

      Journal of Pathology Informatics 2013 4(1):1-1

      Background: Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX TM mass spectrometer to our Sunquest&#174; LIS. Materials and Methods: We licensed software for the data management interface from the University of Pittsburgh, but extended this work as follows: The interface was designed so that it would accept a text file exported from the AB SCIEX TM &#215; 5500 QTrap&#174; mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest&#174; via file transfer protocol. Results: The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst&#174; software to the required Sunquest&#174; import format. This required writing of a "pre-processor" by one of the authors which was easily integrated with the supplied software. Conclusions: We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.
      Citation: Journal of Pathology Informatics 2013 4(1):1-1
      PubDate: Thu,31 Jan 2013
      DOI: 10.4103/2153-3539.106682
      Issue No: Vol. 4, No. 1 (2013)
       
  • Application of whole slide image markup and annotation for pathologist
           knowledge capture
    • Authors: Walter S Campbell, Kirk W Foster, Steven H Hinrichs
      Pages: 2 - 2
      Abstract: Walter S Campbell, Kirk W Foster, Steven H Hinrichs

      Journal of Pathology Informatics 2013 4(1):2-2

      Objective: The ability to transfer image markup and annotation data from one scanned image of a slide to a newly acquired image of the same slide within a single vendor platform was investigated. The goal was to study the ability to use image markup and annotation data files as a mechanism to capture and retain pathologist knowledge without retaining the entire whole slide image (WSI) file. Methods: Accepted mathematical principles were investigated as a method to overcome variations in scans of the same glass slide and to accurately associate image markup and annotation data across different WSI of the same glass slide. Trilateration was used to link fixed points within the image and slide to the placement of markups and annotations of the image in a metadata file. Results: Variation in markup and annotation placement between WSI of the same glass slide was reduced from over 80 &#956; to less than 4 &#956; in the x-axis and from 17 &#956; to 6 &#956; in the y-axis ( P < 0.025). Conclusion: This methodology allows for the creation of a highly reproducible image library of histopathology images and interpretations for educational and research use.
      Citation: Journal of Pathology Informatics 2013 4(1):2-2
      PubDate: Thu,28 Feb 2013
      DOI: 10.4103/2153-3539.107953
      Issue No: Vol. 4, No. 1 (2013)
       
  • Digital pathology: Attitudes and practices in the Canadian pathology
           community
    • Authors: Magdaleni Bellis, Shereen Metias, Christopher Naugler, Aaron Pollett, Serge Jothy, George M Yousef
      Pages: 3 - 3
      Abstract: Magdaleni Bellis, Shereen Metias, Christopher Naugler, Aaron Pollett, Serge Jothy, George M Yousef

      Journal of Pathology Informatics 2013 4(1):3-3

      Digital pathology is a rapidly evolving niche in the world of pathology and is likely to increase in popularity as technology improves. We performed a questionnaire for pathologists and pathology residents across Canada, in order to determine their current experiences and attitudes towards digital pathology; which modalities digital pathology is best suited for; and to assess the need for training in digital pathology amongst pathology residents and staff. An online survey consisting of 24 yes/no, multiple choice and free text questions regarding digital pathology was sent out via E-mail to all members of the Canadian Association of Pathologists and pathology residents across Canada. Survey results showed that telepathology (TP) is used in approximately 43% of institutions, primarily for teaching purposes (65%), followed by operating room consults (46%). Seventy-one percent of respondents believe there is a need for TP in their practice; 85% use digital images in their practice. The top two favored applications for digital pathology are teaching and consultation services, with the main advantage being easier access to cases. The main limitations of using digital pathology are cost and image/diagnostic quality. Sixty-two percent of respondents would attend training courses in pathology informatics and 91% think informatics should be part of residency training. The results of the survey indicate that Pathologists and residents across Canada do see a need for TP and the use of digital images in their daily practice. Integration of an informatics component into resident training programs and courses for staff Pathologists would be welcomed.
      Citation: Journal of Pathology Informatics 2013 4(1):3-3
      PubDate: Thu,14 Mar 2013
      DOI: 10.4103/2153-3539.108540
      Issue No: Vol. 4, No. 1 (2013)
       
  • Privacy and security of patient data in the pathology laboratory
    • Authors: Ioan C Cucoranu, Anil V Parwani, Andrew J West, Gonzalo Romero-Lauro, Kevin Nauman, Alexis B Carter, Ulysses J Balis, Mark J Tuthill, Liron Pantanowitz
      Pages: 4 - 4
      Abstract: Ioan C Cucoranu, Anil V Parwani, Andrew J West, Gonzalo Romero-Lauro, Kevin Nauman, Alexis B Carter, Ulysses J Balis, Mark J Tuthill, Liron Pantanowitz

      Journal of Pathology Informatics 2013 4(1):4-4

      Data protection and security are critical components of routine pathology practice because laboratories are legally required to securely store and transmit electronic patient data. With increasing connectivity of information systems, laboratory work-stations, and instruments themselves to the Internet, the demand to continuously protect and secure laboratory information can become a daunting task. This review addresses informatics security issues in the pathology laboratory related to passwords, biometric devices, data encryption, internet security, virtual private networks, firewalls, anti-viral software, and emergency security situations, as well as the potential impact that newer technologies such as mobile devices have on the privacy and security of electronic protected health information (ePHI). In the United States, the Health Insurance Portability and Accountability Act (HIPAA) govern the privacy and protection of medical information and health records. The HIPAA security standards final rule mandate administrative, physical, and technical safeguards to ensure the confidentiality, integrity, and security of ePHI. Importantly, security failures often lead to privacy breaches, invoking the HIPAA privacy rule as well. Therefore, this review also highlights key aspects of HIPAA and its impact on the pathology laboratory in the United States.
      Citation: Journal of Pathology Informatics 2013 4(1):4-4
      PubDate: Thu,14 Mar 2013
      DOI: 10.4103/2153-3539.108542
      Issue No: Vol. 4, No. 1 (2013)
       
  • A high-performance spatial database based approach for pathology imaging
           algorithm evaluation
    • Authors: Fusheng Wang, Jun Kong, Jingjing Gao, Lee A.D. Cooper, Tahsin Kurc, Zhengwen Zhou, David Adler, Cristobal Vergara-Niedermayr, Bryan Katigbak, Daniel J Brat, Joel H Saltz
      Pages: 5 - 5
      Abstract: Fusheng Wang, Jun Kong, Jingjing Gao, Lee A.D. Cooper, Tahsin Kurc, Zhengwen Zhou, David Adler, Cristobal Vergara-Niedermayr, Bryan Katigbak, Daniel J Brat, Joel H Saltz

      Journal of Pathology Informatics 2013 4(1):5-5

      Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation.
      Citation: Journal of Pathology Informatics 2013 4(1):5-5
      PubDate: Thu,14 Mar 2013
      DOI: 10.4103/2153-3539.108543
      Issue No: Vol. 4, No. 1 (2013)
       
  • A meta-analysis of telemedicine success in Africa
    • Authors: Dan S Wamala, Kaddu Augustine
      Pages: 6 - 6
      Abstract: Dan S Wamala, Kaddu Augustine

      Journal of Pathology Informatics 2013 4(1):6-6

      The use of information and communication technologies (ICT) tools to improve the efficiency of professionalism at work is increasing every time under the dynamic digital environment. Tools such as telemedicine, tele-education, and health informatics have of late been incorporated in the health sector to enable easy access to essential services, for example, in medical areas from referral centers by the patients on one hand and enabling the doctor to doctor consultations for the benefit of patients. Unfortunately, observations indicate dearth efforts and commitment to optimize use of the tools in the majority of the countries south of the Sahara. Sub-Saharan Africa has been left almost behind the rest of the world in terms of development going through decades of economic exploitation by especially the west through its natural and human resources. These factors, ethnic conflicts and endless wars have continued to ruin sub-Saharan Africa's socio-economic development. Information was obtained through a network of telemedicine practitioners in different African countries using internet communication, through E-mail and reviewing existing literature of their activities. This information was compiled from representative countries in each African region and the previous authors'experiences as telemedicine practioners. Most of these countries have inadequate ICT infrastructure, which yet creates sub-optimal application. Sub-Saharan Africa, made up of 33 of the 48 global poorest countries has to extend its ICT diffusion and policy to match the ever developing global economy. In some countries such as Ethiopia and South Africa there is significant progress in Telemedicine while in countries such as Burkina Faso and Nigeria the progress is slow because of lack of political support. Almost all reference to Africa is made in due respect to sub-Saharan Africa, one with big social, economic, and political problems with resultant high morbidity and mortality rates. This also highlights the under-representation of African researchers in the global whelm of information system research. Telemedicine in Africa though has not attracted enough political support is potentially a very useful conduit of health-care given the fact that the continent is resource limited and still enduring the effects of scarce human resource especially in health.
      Citation: Journal of Pathology Informatics 2013 4(1):6-6
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112686
      Issue No: Vol. 4, No. 1 (2013)
       
  • The history of pathology informatics: A global perspective
    • Authors: Seung Park, Anil V Parwani, Raymond D Aller, Lech Banach, Michael J Becich, Stephan Borkenfeld, Alexis B Carter, Bruce A Friedman, Marcial Garcia Rojo, Andrew Georgiou, Gian Kayser, Klaus Kayser, Michael Legg, Christopher Naugler, Takashi Sawai, Hal Weiner, Dennis Winsten, Liron Pantanowitz
      Pages: 7 - 7
      Abstract: Seung Park, Anil V Parwani, Raymond D Aller, Lech Banach, Michael J Becich, Stephan Borkenfeld, Alexis B Carter, Bruce A Friedman, Marcial Garcia Rojo, Andrew Georgiou, Gian Kayser, Klaus Kayser, Michael Legg, Christopher Naugler, Takashi Sawai, Hal Weiner, Dennis Winsten, Liron Pantanowitz

      Journal of Pathology Informatics 2013 4(1):7-7

      Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold.
      Citation: Journal of Pathology Informatics 2013 4(1):7-7
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112689
      Issue No: Vol. 4, No. 1 (2013)
       
  • Mitosis detection in breast cancer histological images An ICPR 2012
           contest
    • Authors: Ludovic Roux, Daniel Racoceanu, Nicolas Loménie, Maria Kulikova, Humayun Irshad, Jacques Klossa, Frédérique Capron, Catherine Genestie, Gilles Le Naour, Metin N Gurcan
      Pages: 8 - 8
      Abstract: Ludovic Roux, Daniel Racoceanu, Nicolas Loménie, Maria Kulikova, Humayun Irshad, Jacques Klossa, Frédérique Capron, Catherine Genestie, Gilles Le Naour, Metin N Gurcan

      Journal of Pathology Informatics 2013 4(1):8-8

      Introduction: In the framework of the Cognitive Microscope (MICO) project, we have set up a contest about mitosis detection in images of H and E stained slides of breast cancer for the conference ICPR 2012. Mitotic count is an important parameter for the prognosis of breast cancer. However, mitosis detection in digital histopathology is a challenging problem that needs a deeper study. Indeed, mitosis detection is difficult because mitosis are small objects with a large variety of shapes, and they can thus be easily confused with some other objects or artefacts present in the image. We added a further dimension to the contest by using two different slide scanners having different resolutions and producing red-green-blue (RGB) images, and a multi-spectral microscope producing images in 10 different spectral bands and 17 layers Z-stack. 17 teams participated in the study and the best team achieved a recall rate of 0.7 and precision of 0.89. Context: Several studies on automatic tools to process digitized slides have been reported focusing mainly on nuclei or tubule detection. Mitosis detection is a challenging problem that has not yet been addressed well in the literature. Aims: Mitotic count is an important parameter in breast cancer grading as it gives an evaluation of the aggressiveness of the tumor. However, consistency, reproducibility and agreement on mitotic count for the same slide can vary largely among pathologists. An automatic tool for this task may help for reaching a better consistency, and at the same time reducing the burden of this demanding task for the pathologists. Subjects and Methods: Professor Fr&#953;d&#953;rique Capron team of the pathology department at Piti&#953;-Salp&#954;tri&#952;re Hospital in Paris, France, has selected a set of five slides of breast cancer. The slides are stained with H and E. They have been scanned by three different equipments: Aperio ScanScope XT slide scanner, Hamamatsu NanoZoomer 2.0-HT slide scanner and 10 bands multispectral microscope. The data set is made up of 50 high power fields (HPF) coming from 5 different slides scanned at &#215;40 magnification. There are 10 HPFs/slide. The pathologist has annotated all the mitotic cells manually. A HPF has a size of 512 &#956;m &#215; 512 &#956;m (that is an area of 0.262 mm 2 , which is a surface equivalent to that of a microscope field diameter of 0.58 mm. These 50 HPFs contain a total of 326 mitotic cells on images of both scanners, and 322 mitotic cells on the multispectral microscope. Results : Up to 129 teams have registered to the contest. However, only 17 teams submitted their detection of mitotic cells. The performance of the best team is very promising, with F-measure as high as 0.78. However, the database we provided is by far too small for a good assessment of reliability and robustness of the proposed algorithms. Conclusions : Mitotic count is an important criterion in the grading of many types of cancers, however, very little research has been made on automatic mitotic cell detection, mainly because of a lack of available data. A main objective of this contest was to propose a database of mitotic cells on digitized breast cancer histopathology slides to initiate works on automated mitotic cell detection. In the future, we would like to extend this database to have much more images from different patients and also for different types of cancers. In addition, mitotic cells should be annotated by several pathologists to reflect the partial agreement among them.
      Citation: Journal of Pathology Informatics 2013 4(1):8-8
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112693
      Issue No: Vol. 4, No. 1 (2013)
       
  • Classification of mitotic figures with convolutional neural networks and
           seeded blob features
    • Authors: Christopher D Malon, Eric Cosatto
      Pages: 9 - 9
      Abstract: Christopher D Malon, Eric Cosatto

      Journal of Pathology Informatics 2013 4(1):9-9

      Background: The mitotic figure recognition contest at the 2012 International Conference on Pattern Recognition (ICPR) challenges a system to identify all mitotic figures in a region of interest of hematoxylin and eosin stained tissue, using each of three scanners (Aperio, Hamamatsu, and multispectral). Methods: Our approach combines manually designed nuclear features with the learned features extracted by convolutional neural networks (CNN). The nuclear features capture color, texture, and shape information of segmented regions around a nucleus. The use of a CNN handles the variety of appearances of mitotic figures and decreases sensitivity to the manually crafted features and thresholds. Results : On the test set provided by the contest, the trained system achieves F1 scores up to 0.659 on color scanners and 0.589 on multispectral scanner. Conclusions : We demonstrate a powerful technique combining segmentation-based features with CNN, identifying the majority of mitotic figures with a fair precision. Further, we show that the approach accommodates information from the additional focal planes and spectral bands from a multi-spectral scanner without major redesign.
      Citation: Journal of Pathology Informatics 2013 4(1):9-9
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112694
      Issue No: Vol. 4, No. 1 (2013)
       
  • Automated mitosis detection in histopathology using morphological and
           multi-channel statistics features
    • Authors: Humayun Irshad
      Pages: 10 - 10
      Abstract: Humayun Irshad

      Journal of Pathology Informatics 2013 4(1):10-10

      Context: According to Nottingham grading system, mitosis count plays a critical role in cancer diagnosis and grading. Manual counting of mitosis is tedious and subject to considerable inter- and intra-reader variations. Aims: The aim is to improve the accuracy of mitosis detection by selecting the color channels that better capture the statistical and morphological features, which classify mitosis from other objects. Materials and Methods: We propose a framework that includes comprehensive analysis of statistics and morphological features in selected channels of various color spaces that assist pathologists in mitosis detection. In candidate detection phase, we perform Laplacian of Gaussian, thresholding, morphology and active contour model on blue-ratio image to detect and segment candidates. In candidate classification phase, we extract a total of 143 features including morphological, first order and second order (texture) statistics features for each candidate in selected channels and finally classify using decision tree classifier. Results and Discussion: The proposed method has been evaluated on Mitosis Detection in Breast Cancer Histological Images (MITOS) dataset provided for an International Conference on Pattern Recognition 2012 contest and achieved 74% and 71% detection rate, 70% and 56% precision and 72% and 63% F-Measure on Aperio and Hamamatsu images, respectively. Conclusions and Future Work: The proposed multi-channel features computation scheme uses fixed image scale and extracts nuclei features in selected channels of various color spaces. This simple but robust model has proven to be highly efficient in capturing multi-channels statistical features for mitosis detection, during the MITOS international benchmark. Indeed, the mitosis detection of critical importance in cancer diagnosis is a very challenging visual task. In future work, we plan to use color deconvolution as preprocessing and Hough transform or local extrema based candidate detection in order to reduce the number of candidates in mitosis and non-mitosis classes.
      Citation: Journal of Pathology Informatics 2013 4(1):10-10
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112695
      Issue No: Vol. 4, No. 1 (2013)
       
  • A gamma-gaussian mixture model for detection of mitotic cells in breast
           cancer histopathology images
    • Authors: Adnan Mujahid Khan, Hesham ElDaly, Nasir M Rajpoot
      Pages: 11 - 11
      Abstract: Adnan Mujahid Khan, Hesham ElDaly, Nasir M Rajpoot

      Journal of Pathology Informatics 2013 4(1):11-11

      In this paper, we propose a statistical approach for mitosis detection in breast cancer histological images. The proposed algorithm models the pixel intensities in mitotic and non-mitotic regions by a Gamma-Gaussian mixture model (GGMM) and employs a context aware post-processing (CAPP) in order to reduce false positives. Experimental results demonstrate the ability of this simple, yet effective method to detect mitotic cells (MCs) in standard H & E breast cancer histology images. Context: Counting of MCs in breast cancer histopathology images is one of three components (the other two being tubule formation, nuclear pleomorphism) required for developing computer assisted grading of breast cancer tissue slides. This is very challenging since the biological variability of the MCs makes their detection extremely difficult. In addition, if standard H & E is used (which stains chromatin rich structures, such as nucleus, apoptotic, and MCs dark blue) and it becomes extremely difficult to detect the latter given the fact that former two are densely localized in the tissue sections. Aims: In this paper, a robust MCs detection technique is developed and tested on 35 breast histopathology images, belonging to five different tissue slides. Settings and Design: Our approach mimics a pathologists' approach to MCs detections. The idea is (1) to isolate tumor areas from non-tumor areas (lymphoid/inflammatory/apoptotic cells), (2) search for MCs in the reduced space by statistically modeling the pixel intensities from mitotic and non-mitotic regions, and finally (3) evaluate the context of each potential MC in terms of its texture. Materials and Methods: Our experimental dataset consisted of 35 digitized images of breast cancer biopsy slides with paraffin embedded sections stained with H and E and scanned at &#215; 40 using an Aperio scanscope slide scanner. Statistical Analysis Used: We propose GGMM for detecting MCs in breast histology images. Image intensities are modeled as random variables sampled from one of the two distributions; Gamma and Gaussian. Intensities from MCs are modeled by a gamma distribution and those from non-mitotic regions are modeled by a gaussian distribution. The choice of Gamma-Gaussian distribution is mainly due to the observation that the characteristics of the distribution match well with the data it models. The experimental results show that the proposed system achieves a high sensitivity of 0.82 with positive predictive value (PPV) of 0.29. Employing CAPP on these results produce 241% increase in PPV at the cost of less than 15% decrease in sensitivity. Conclusions: In this paper, we presented a GGMM for detection of MCs in breast cancer histopathological images. In addition, we introduced CAPP as a tool to increase the PPV with a minimal loss in sensitivity. We evaluated the performance of the proposed detection algorithm in terms of sensitivity and PPV over a set of 35 breast histology images selected from five different tissue slides and showed that a reasonably high value of sensitivity can be retained while increasing the PPV. Our future work will aim at increasing the PPV further by modeling the spatial appearance of regions surrounding mitotic events.
      Citation: Journal of Pathology Informatics 2013 4(1):11-11
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112696
      Issue No: Vol. 4, No. 1 (2013)
       
  • Mitosis detection using generic features and an ensemble of cascade
           adaboosts
    • Authors: F Boray Tek
      Pages: 12 - 12
      Abstract: F Boray Tek

      Journal of Pathology Informatics 2013 4(1):12-12

      Context: Mitosis count is one of the factors that pathologists use to assess the risk of metastasis and survival of the patients, which are affected by the breast cancer. Aims: We investigate an application of a set of generic features and an ensemble of cascade adaboosts to the automated mitosis detection. Calculation of the features rely minimally on object-level descriptions and thus require minimal segmentation. Materials and Methods: The proposed work was developed and tested on International Conference on Pattern Recognition (ICPR) 2012 mitosis detection contest data. Statistical Analysis Used: We plotted receiver operating characteristics curves of true positive versus false positive rates; calculated recall, precision, F-measure, and region overlap ratio measures. Results: We tested our features with two different classifier configurations: 1) An ensemble of single adaboosts, 2) an ensemble of cascade adaboosts. On the ICPR 2012 mitosis detection contest evaluation, the cascade ensemble scored 54, 62.7, and 58, whereas the non-cascade version scored 68, 28.1, and 39.7 for the recall, precision, and F-measure measures, respectively. Mostly used features in the adaboost classifier rules were a shape-based feature, which counted granularity and a color-based feature, which relied on Red, Green, and Blue channel statistics. Conclusions: The features, which express the granular structure and color variations, are found useful for mitosis detection. The ensemble of adaboosts performs better than the individual adaboost classifiers. Moreover, the ensemble of cascaded adaboosts was better than the ensemble of single adaboosts for mitosis detection.
      Citation: Journal of Pathology Informatics 2013 4(1):12-12
      PubDate: Thu,30 May 2013
      DOI: 10.4103/2153-3539.112697
      Issue No: Vol. 4, No. 1 (2013)
       
  • The (not yet) willingly adopted tool
    • Authors: Lewis A Hassell, Eric Glassy
      Pages: 13 - 13
      Abstract: Lewis A Hassell, Eric Glassy

      Journal of Pathology Informatics 2013 4(1):13-13


      Citation: Journal of Pathology Informatics 2013 4(1):13-13
      PubDate: Sat,29 Jun 2013
      DOI: 10.4103/2153-3539.114204
      Issue No: Vol. 4, No. 1 (2013)
       
  • Performance of CellaVision DM96 in leukocyte classification
    • Authors: Lik Hang Lee, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Christopher Naugler
      Pages: 14 - 14
      Abstract: Lik Hang Lee, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Christopher Naugler

      Journal of Pathology Informatics 2013 4(1):14-14

      Background: Leukocyte differentials are an important component of clinical care. Morphologic assessment of peripheral blood smears (PBS) may be required to accurately classify leukocytes. However, manual microscopy is labor intensive. The CellaVision DM96 is an automated system that acquires digital images of leukocytes on PBS, pre-classifies the cell type, and displays them on screen for a Technologist or Pathologist to approve or reclassify. Our study compares the results of the DM96 with manual microscopy. Methods: Three hundred and fifty-nine PBS were selected and assessed by manual microscopy with a 200 leukocyte cell count. They were then reassessed using the CellaVision DM96 with a 115 leukocyte cell count including reclassification when necessary. Correlation between the manual microscopy results and the CellaVision DM96 results was calculated for each cell type. Results: The correlation coefficients (r2 ) range from a high of 0.99 for blasts to a low of 0.72 for metamyelocytes. Conclusions: The correlation between the CellaVision DM96 and manual microscopy was as good or better than the previously published data. The accuracy of leukocyte classification depended on the cell type, and in general, there was lower correlation for rare cell types. However, the correlation is similar to previous studies on the correlation of manual microscopy with an established reference result. Therefore, the CellaVision DM96 is appropriate for clinical implementation.
      Citation: Journal of Pathology Informatics 2013 4(1):14-14
      PubDate: Sat,29 Jun 2013
      DOI: 10.4103/2153-3539.114205
      Issue No: Vol. 4, No. 1 (2013)
       
  • Going fully digital: Perspective of a Dutch academic pathology lab
    • Authors: Nikolas Stathonikos, Mitko Veta, André Huisman, Paul J van Diest
      Pages: 15 - 15
      Abstract: Nikolas Stathonikos, Mitko Veta, André Huisman, Paul J van Diest

      Journal of Pathology Informatics 2013 4(1):15-15

      During the last years, whole slide imaging has become more affordable and widely accepted in pathology labs. Digital slides are increasingly being used for digital archiving of routinely produced clinical slides, remote consultation and tumor boards, and quantitative image analysis for research purposes and in education. However, the implementation of a fully digital Pathology Department requires an in depth look into the suitability of digital slides for routine clinical use (the image quality of the produced digital slides and the factors that affect it) and the required infrastructure to support such use (the storage requirements and integration with lab management and hospital information systems). Optimization of digital pathology workflow requires communication between several systems, which can be facilitated by the use of open standards for digital slide storage and scanner management. Consideration of these aspects along with appropriate validation of the use of digital slides for routine pathology can pave the way for pathology departments to go "fully digital." In this paper, we summarize our experiences so far in the process of implementing a fully digital workflow at our Pathology Department and the steps that are needed to complete this process.
      Citation: Journal of Pathology Informatics 2013 4(1):15-15
      PubDate: Sat,29 Jun 2013
      DOI: 10.4103/2153-3539.114206
      Issue No: Vol. 4, No. 1 (2013)
       
  • Platelet count estimation using the CellaVision DM96 system
    • Authors: Yuon Gao, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Christopher Naugler
      Pages: 16 - 16
      Abstract: Yuon Gao, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Christopher Naugler

      Journal of Pathology Informatics 2013 4(1):16-16

      Introduction: Rapid and accurate determination of platelet count is an important factor in diagnostic medicine. Traditional microscopic methods are labor intensive with variable results and are highly dependent on the individual training. Recent developments in automated peripheral blood differentials using a computerized system have shown many advantages as a viable alternative. The purpose of this paper was to determine the reliability and accuracy of the CellaVision DM 96 system with regards to platelet counts. Materials and Methods: One hundred twenty seven peripheral blood smears were analyzed for platelet count by manual microscopy, an automated hematology analyzer (Beckman Counter LH 780 or Unicel DXH 800 analyzers) and with the CellaVision DM96 system. Results were compared using the correlations and Bland-Altman plots. Results: Platelet counts from the DM96 system showed an R 2 of 0.94 when compared to manual platelet estimates and an R 2 of 0.92 when compared to the automated hematology analyzer results. Bland-Altman plots did not show any systematic bias.
      Citation: Journal of Pathology Informatics 2013 4(1):16-16
      PubDate: Sat,29 Jun 2013
      DOI: 10.4103/2153-3539.114207
      Issue No: Vol. 4, No. 1 (2013)
       
  • Review of "Digital image forensics: There is more to a picture than
           meets the eye" by Husrev Taha Sencar and Nasir Memon (Editors)
    • Authors: Bruce Levy
      Pages: 17 - 17
      Abstract: Bruce Levy

      Journal of Pathology Informatics 2013 4(1):17-17


      Citation: Journal of Pathology Informatics 2013 4(1):17-17
      PubDate: Sat,29 Jun 2013
      Issue No: Vol. 4, No. 1 (2013)
       
  • What is new in the evaluation of diagnostic digital cytopathology in
           cervicovaginal smears?
    • Authors: Marilyn M Bui, Corinne L Stephenson
      Pages: 18 - 18
      Abstract: Marilyn M Bui, Corinne L Stephenson

      Journal of Pathology Informatics 2013 4(1):18-18


      Citation: Journal of Pathology Informatics 2013 4(1):18-18
      PubDate: Wed,31 Jul 2013
      DOI: 10.4103/2153-3539.115874
      Issue No: Vol. 4, No. 1 (2013)
       
  • Reproducibility in the automated quantitative assessment of HER2/neu for
           breast cancer
    • Authors: Tyler Keay, Catherine Conway, Neil O'Flaherty, Stephen M Hewitt, Katherine Shea, Marios A Gavrielides
      Pages: 19 - 19
      Abstract: Tyler Keay, Catherine Conway, Neil O'Flaherty, Stephen M Hewitt, Katherine Shea, Marios A Gavrielides

      Journal of Pathology Informatics 2013 4(1):19-19

      Background: With the emerging role of digital imaging in pathology and the application of automated image-based algorithms to a number of quantitative tasks, there is a need to examine factors that may affect the reproducibility of results. These factors include the imaging properties of whole slide imaging (WSI) systems and their effect on the performance of quantitative tools. This manuscript examines inter-scanner and inter-algorithm variability in the assessment of the commonly used HER2/neu tissue-based biomarker for breast cancer with emphasis on the effect of algorithm training. Materials and Methods: A total of 241 regions of interest from 64 breast cancer tissue glass slides were scanned using three different whole-slide images and were analyzed using two different automated image analysis algorithms, one with preset parameters and another incorporating a procedure for objective parameter optimization. Ground truth from a panel of seven pathologists was available from a previous study. Agreement analysis was used to compare the resulting HER2/neu scores. Results: The results of our study showed that inter-scanner agreement in the assessment of HER2/neu for breast cancer in selected fields of view when analyzed with any of the two algorithms examined in this study was equal or better than the inter-observer agreement previously reported on the same set of data. Results also showed that discrepancies observed between algorithm results on data from different scanners were significantly reduced when the alternative algorithm that incorporated an objective re-training procedure was used, compared to the commercial algorithm with preset parameters. Conclusion: Our study supports the use of objective procedures for algorithm training to account for differences in image properties between WSI systems.
      Citation: Journal of Pathology Informatics 2013 4(1):19-19
      PubDate: Wed,31 Jul 2013
      DOI: 10.4103/2153-3539.115879
      Issue No: Vol. 4, No. 1 (2013)
       
  • Automated extraction of precise protein expression patterns in lymphoma by
           text mining abstracts of immunohistochemical studies
    • Authors: Jia-Fu Chang, Mihail Popescu, Gerald L Arthur
      Pages: 20 - 20
      Abstract: Jia-Fu Chang, Mihail Popescu, Gerald L Arthur

      Journal of Pathology Informatics 2013 4(1):20-20

      Background: In general, surgical pathology reviews report protein expression by tumors in a semi-quantitative manner, that is, -, -/+, +/-, +. At the same time, the experimental pathology literature provides multiple examples of precise expression levels determined by immunohistochemical (IHC) tissue examination of populations of tumors. Natural language processing (NLP) techniques enable the automated extraction of such information through text mining. We propose establishing a database linking quantitative protein expression levels with specific tumor classifications through NLP. Materials and Methods: Our method takes advantage of typical forms of representing experimental findings in terms of percentages of protein expression manifest by the tumor population under study. Characteristically, percentages are represented straightforwardly with the % symbol or as the number of positive findings of the total population. Such text is readily recognized using regular expressions and templates permitting extraction of sentences containing these forms for further analysis using grammatical structures and rule-based algorithms. Results: Our pilot study is limited to the extraction of such information related to lymphomas. We achieved a satisfactory level of retrieval as reflected in scores of 69.91% precision and 57.25% recall with an F-score of 62.95%. In addition, we demonstrate the utility of a web-based curation tool for confirming and correcting our findings. Conclusions: The experimental pathology literature represents a rich source of pathobiological information, which has been relatively underutilized. There has been a combinatorial explosion of knowledge within the pathology domain as represented by increasing numbers of immunophenotypes and disease subclassifications. NLP techniques support practical text mining techniques for extracting this knowledge and organizing it in forms appropriate for pathology decision support systems.
      Citation: Journal of Pathology Informatics 2013 4(1):20-20
      PubDate: Wed,31 Jul 2013
      DOI: 10.4103/2153-3539.115880
      Issue No: Vol. 4, No. 1 (2013)
       
  • Relationship between magnification and resolution in digital pathology
           systems
    • Authors: Tiffany L Sellaro, Robert Filkins, Chelsea Hoffman, Jeffrey L Fine, Jon Ho, Anil V Parwani, Liron Pantanowitz, Michael Montalto
      Pages: 21 - 21
      Abstract: Tiffany L Sellaro, Robert Filkins, Chelsea Hoffman, Jeffrey L Fine, Jon Ho, Anil V Parwani, Liron Pantanowitz, Michael Montalto

      Journal of Pathology Informatics 2013 4(1):21-21

      Many pathology laboratories are implementing digital pathology systems. The image resolution and scanning (digitization) magnification can vary greatly between these digital pathology systems. In addition, when digital images are compared with viewing images using a microscope, the cellular features can vary in size. This article highlights differences in magnification and resolution between the conventional microscopes and the digital pathology systems. As more pathologists adopt digital pathology, it is important that they understand these differences and how they ultimately translate into what the pathologist can see and how this may impact their overall viewing experience.
      Citation: Journal of Pathology Informatics 2013 4(1):21-21
      PubDate: Thu,22 Aug 2013
      DOI: 10.4103/2153-3539.116866
      Issue No: Vol. 4, No. 1 (2013)
       
  • Eliminating tissue-fold artifacts in histopathological whole-slide images
           for improved image-based prediction of cancer grade
    • Authors: Sonal Kothari, John H Phan, May D Wang
      Pages: 22 - 22
      Abstract: Sonal Kothari, John H Phan, May D Wang

      Journal of Pathology Informatics 2013 4(1):22-22

      Background: Analysis of tissue biopsy whole-slide images (WSIs) depends on effective detection and elimination of image artifacts. We present a novel method to detect tissue-fold artifacts in histopathological WSIs. We also study the effect of tissue folds on image features and prediction models. Materials and Methods: We use WSIs of samples from two cancer endpoints - kidney clear cell carcinoma (KiCa) and ovarian serous adenocarcinoma (OvCa) - publicly available from The Cancer Genome Atlas. We detect tissue folds in low-resolution WSIs using color properties and two adaptive connectivity-based thresholds. We optimize and validate our tissue-fold detection method using 105 manually annotated WSIs from both cancer endpoints. In addition to detecting tissue folds, we extract 461 image features from the high-resolution WSIs for all samples. We use the rank-sum test to find image features that are statistically different among features extracted from the same set of WSIs with and without folds. We then use features that are affected by tissue folds to develop models for predicting cancer grades. Results: When compared to the ground truth, our method detects tissue folds in KiCa with 0.50 adjusted Rand index (ARI), 0.77 average true rate (ATR), 0.55 true positive rate (TPR), and 0.98 true negative rate (TNR); and in OvCa with 0.40 ARI, 0.73 ATR, 0.47 TPR, and 0.98 TNR. Compared to two other methods, our method is more accurate in terms of ARI and ATR. We found that 53 and 30 image features were significantly affected by the presence of tissue-fold artifacts (detected using our method) in OvCa and KiCa, respectively. After eliminating tissue folds, the performance of cancer-grade prediction models improved by 5% and 1% in OvCa and KiCa, respectively. Conclusion: The proposed connectivity-based method is more effective in detecting tissue folds compared to other methods. Reducing tissue-fold artifacts will increase the performance of cancer-grade prediction models.
      Citation: Journal of Pathology Informatics 2013 4(1):22-22
      PubDate: Sat,31 Aug 2013
      DOI: 10.4103/2153-3539.117448
      Issue No: Vol. 4, No. 1 (2013)
       
  • Extracting laboratory test information from biomedical text
    • Authors: Yanna Shen Kang, Mehmet Kayaalp
      Pages: 23 - 23
      Abstract: Yanna Shen Kang, Mehmet Kayaalp

      Journal of Pathology Informatics 2013 4(1):23-23

      Background: No previous study reported the efficacy of current natural language processing (NLP) methods for extracting laboratory test information from narrative documents. This study investigates the pathology informatics question of how accurately such information can be extracted from text with the current tools and techniques, especially machine learning and symbolic NLP methods. The study data came from a text corpus maintained by the U.S. Food and Drug Administration, containing a rich set of information on laboratory tests and test devices. Methods: The authors developed a symbolic information extraction (SIE) system to extract device and test specific information about four types of laboratory test entities: Specimens, analytes, units of measures and detection limits. They compared the performance of SIE and three prominent machine learning based NLP systems, LingPipe, GATE and BANNER, each implementing a distinct supervised machine learning method, hidden Markov models, support vector machines and conditional random fields, respectively. Results: Machine learning systems recognized laboratory test entities with moderately high recall, but low precision rates. Their recall rates were relatively higher when the number of distinct entity values (e.g., the spectrum of specimens) was very limited or when lexical morphology of the entity was distinctive (as in units of measures), yet SIE outperformed them with statistically significant margins on extracting specimen, analyte and detection limit information in both precision and F-measure. Its high recall performance was statistically significant on analyte information extraction. Conclusions: Despite its shortcomings against machine learning methods, a well-tailored symbolic system may better discern relevancy among a pile of information of the same type and may outperform a machine learning system by tapping into lexically non-local contextual information such as the document structure.
      Citation: Journal of Pathology Informatics 2013 4(1):23-23
      PubDate: Sat,31 Aug 2013
      DOI: 10.4103/2153-3539.117450
      Issue No: Vol. 4, No. 1 (2013)
       
  • World's first telepathology experiments employing ultra-high-speed
           internet satellite, nicknamed "KIZUNA"
    • Authors: Takashi Sawai, Miwa Uzuki, Yasuhiro Miura, Akihisa Kamataki, Tsubasa Matsumura, Kenji Saito, Akira Kurose, Yoshiyuki R Osamura, Naoki Yoshimi, Hiroyuki Kanno, Takuya Moriya, Yoji Ishida, Yohichi Satoh, Masahiro Nakao, Emiko Ogawa, Satoshi Matsuo, Hiroyuki Kasai, Kazuhiro Kumagai, Toshihiro Motoda, Nathan Hopson
      Pages: 24 - 24
      Abstract: Takashi Sawai, Miwa Uzuki, Yasuhiro Miura, Akihisa Kamataki, Tsubasa Matsumura, Kenji Saito, Akira Kurose, Yoshiyuki R Osamura, Naoki Yoshimi, Hiroyuki Kanno, Takuya Moriya, Yoji Ishida, Yohichi Satoh, Masahiro Nakao, Emiko Ogawa, Satoshi Matsuo, Hiroyuki Kasai, Kazuhiro Kumagai, Toshihiro Motoda, Nathan Hopson

      Journal of Pathology Informatics 2013 4(1):24-24

      Background: Recent advances in information technology have allowed the development of a telepathology system involving high-speed transfer of high-volume histological figures via fiber optic landlines. However, at present there are geographical limits to landlines. The Japan Aerospace Exploration Agency (JAXA) has developed the "Kizuna" ultra-high speed internet satellite and has pursued its various applications. In this study we experimented with telepathology in collaboration with JAXA using Kizuna. To measure the functionality of the Wideband InterNet working engineering test and Demonstration Satellite (WINDS) ultra-high speed internet satellite in remote pathological diagnosis and consultation, we examined the adequate data transfer speed and stability to conduct telepathology (both diagnosis and conferencing) with functionality, and ease similar or equal to telepathology using fiber-optic landlines. Materials and Methods: We performed experiments for 2 years. In year 1, we tested the usability of the WINDS for telepathology with real-time video and virtual slide systems. These are state-of-the-art technologies requiring massive volumes of data transfer. In year 2, we tested the usability of the WINDS for three-way teleconferencing with virtual slides. Facilities in Iwate (northern Japan), Tokyo, and Okinawa were connected via the WINDS and voice conferenced while remotely examining and manipulating virtual slides. Results: Network function parameters measured using ping and Iperf were within acceptable limits. However; stage movement, zoom, and conversation suffered a lag of approximately 0.8 s when using real-time video, and a delay of 60-90 s was experienced when accessing the first virtual slide in a session. No significant lag or inconvenience was experienced during diagnosis and conferencing, and the results were satisfactory. Our hypothesis was confirmed for both remote diagnosis using real-time video and virtual slide systems, and also for teleconferencing using virtual slide systems with voice functionality. Conclusions: Our results demonstrate the feasibility of ultra-high-speed internet satellite networks for use in telepathology. Because communications satellites have less geographical and infrastructural requirements than landlines, ultra-high-speed internet satellite telepathology represents a major step toward alleviating regional disparity in the quality of medical care.
      Citation: Journal of Pathology Informatics 2013 4(1):24-24
      PubDate: Fri,27 Sep 2013
      DOI: 10.4103/2153-3539.119002
      Issue No: Vol. 4, No. 1 (2013)
       
  • Review of "Next-generation DNA sequencing informatics" by Stuart
           M. Brown (Editor)
    • Authors: Jennifer K Sehn
      Pages: 25 - 25
      Abstract: Jennifer K Sehn

      Journal of Pathology Informatics 2013 4(1):25-25


      Citation: Journal of Pathology Informatics 2013 4(1):25-25
      PubDate: Fri,27 Sep 2013
      Issue No: Vol. 4, No. 1 (2013)
       
  • Full-field optical coherence tomography for the analysis of fresh
           unstained human lobectomy specimens
    • Authors: Manu Jain, Navneet Narula, Bekheit Salamoon, Maria M Shevchuk, Amit Aggarwal, Nasser Altorki, Brendon Stiles, Claude Boccara, Sushmita Mukherjee
      Pages: 26 - 26
      Abstract: Manu Jain, Navneet Narula, Bekheit Salamoon, Maria M Shevchuk, Amit Aggarwal, Nasser Altorki, Brendon Stiles, Claude Boccara, Sushmita Mukherjee

      Journal of Pathology Informatics 2013 4(1):26-26

      Background: Full-field optical coherence tomography (FFOCT) is a real-time imaging technique that generates high-resolution three-dimensional tomographic images from unprocessed and unstained tissues. Lack of tissue processing and associated artifacts, along with the ability to generate large-field images quickly, warrants its exploration as an alternative diagnostic tool. Materials and Methods: One section each from the tumor and from adjacent non-neoplastic tissue was collected from 13 human lobectomy specimens. They were imaged fresh with FFOCT and then submitted for routine histopathology. Two blinded pathologists independently rendered diagnoses based on FFOCT images. Results: Normal lung architecture (alveoli, bronchi, pleura and blood vessels) was readily identified with FFOCT. Using FFOCT images alone, the study pathologists were able to correctly identify all tumor specimens and in many cases, the histological subtype of tumor (e.g., adenocarcinomas with various patterns). However, benign diagnosis was provided with high confidence in roughly half the tumor-free specimens (others were diagnosed as equivocal or false positive). Further analysis of these images revealed two major confounding features: (a) Extensive lung collapse and (b) presence of smoker's macrophages. On a closer inspection, however, the smoker's macrophages could often be identified as distinct from tumor cells based on their relative location in the alveoli, size and presence of anthracosis. We posit that greater pathologist experience, complemented with morphometric analysis and color-coding of image components, may help minimize the contribution of these confounders in the future. Conclusion: Our study provides evidence for the potential utility of FFOCT in identifying and differentiating lung tumors from non-neoplastic lung tissue. We foresee its potential as an adjunct to intra-surgical frozen section analysis for margin assessment, especially in limited lung resections.
      Citation: Journal of Pathology Informatics 2013 4(1):26-26
      PubDate: Fri,27 Sep 2013
      DOI: 10.4103/2153-3539.119004
      Issue No: Vol. 4, No. 1 (2013)
       
  • OpenSlide: A vendor-neutral software foundation for digital pathology
    • Authors: Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, Mahadev Satyanarayanan
      Pages: 27 - 27
      Abstract: Adam Goode, Benjamin Gilbert, Jan Harkes, Drazen Jukic, Mahadev Satyanarayanan

      Journal of Pathology Informatics 2013 4(1):27-27

      Although widely touted as a replacement for glass slides and microscopes in pathology, digital slides present major challenges in data storage, transmission, processing and interoperability. Since no universal data format is in widespread use for these images today, each vendor defines its own proprietary data formats, analysis tools, viewers and software libraries. This creates issues not only for pathologists, but also for interoperability. In this paper, we present the design and implementation of OpenSlide, a vendor-neutral C library for reading and manipulating digital slides of diverse vendor formats. The library is extensible and easily interfaced to various programming languages. An application written to the OpenSlide interface can transparently handle multiple vendor formats. OpenSlide is in use today by many academic and industrial organizations world-wide, including many research sites in the United States that are funded by the National Institutes of Health.
      Citation: Journal of Pathology Informatics 2013 4(1):27-27
      PubDate: Fri,27 Sep 2013
      DOI: 10.4103/2153-3539.119005
      Issue No: Vol. 4, No. 1 (2013)
       
  • Diagnostic digital cytopathology: Are we ready yet?
    • Authors: Jarret C House, Evita B Henderson-Jackson, Joseph O Johnson, Mark C Lloyd, Jasreman Dhillon, Nazeel Ahmad, Ardeshir Hakam, Walid E Khalbuss, Marino E Leon, David Chhieng, Xiaohui Zhang, Barbara A Centeno, Marilyn M Bui
      Pages: 28 - 28
      Abstract: Jarret C House, Evita B Henderson-Jackson, Joseph O Johnson, Mark C Lloyd, Jasreman Dhillon, Nazeel Ahmad, Ardeshir Hakam, Walid E Khalbuss, Marino E Leon, David Chhieng, Xiaohui Zhang, Barbara A Centeno, Marilyn M Bui

      Journal of Pathology Informatics 2013 4(1):28-28

      Background: The cytology literature relating to diagnostic accuracy using whole slide imaging is scarce. We studied the diagnostic concordance between glass and digital slides among diagnosticians with different profiles to assess the readiness of adopting digital cytology in routine practice. Materials and Methods: This cohort consisted of 22 de-identified previously screened and diagnosed cases, including non-gynecological and gynecological slides using standard preparations. Glass slides were digitalized using Aperio ScanScope XT (&#215;20 and &#215;40). Cytopathologists with (3) and without (3) digital experience, cytotechnologists (4) and senior pathology residents (2) diagnosed the digital slides independently first and recorded the results. Glass slides were read and recorded separately 1-3 days later. Accuracy of diagnosis, time to diagnosis and diagnostician's profile were analyzed. Results: Among 22 case pairs and four study groups, correct diagnosis (93% vs. 86%) was established using glass versus digital slides. Both methods more (>95%) accurately diagnosed positive cases than negatives. Cytopathologists with no digital experience were the most accurate in digital diagnosis, even the senior members. Cytotechnologists had the fastest diagnosis time (3 min/digital vs. 1.7 min/glass), but not the best accuracy. Digital time was 1.5 min longer than glass-slide time/per case for cytopathologists and cytotechnologists. Senior pathology residents were slower and less accurate with both methods. Cytopathologists with digital experience ranked 2 nd fastest in time, yet last in accuracy for digital slides. Conclusions: There was good overall diagnostic agreement between the digital whole-slide images and glass slides. Although glass slide diagnosis was more accurate and faster, the results of technologists and pathologists with no digital cytology experience suggest that solid diagnostic ability is a strong indicator for readiness of digital adoption.
      Citation: Journal of Pathology Informatics 2013 4(1):28-28
      PubDate: Tue,29 Oct 2013
      DOI: 10.4103/2153-3539.120727
      Issue No: Vol. 4, No. 1 (2013)
       
  • Development and validation of a tool to evaluate the quality of medical
           education websites in pathology
    • Authors: Raja H Alyusuf, Kameshwar Prasad, Ali M Abdel Satir, Ali A Abalkhail, Roopa K Arora
      Pages: 29 - 29
      Abstract: Raja H Alyusuf, Kameshwar Prasad, Ali M Abdel Satir, Ali A Abalkhail, Roopa K Arora

      Journal of Pathology Informatics 2013 4(1):29-29

      Background: The exponential use of the internet as a learning resource coupled with varied quality of many websites, lead to a need to identify suitable websites for teaching purposes. Aim: The aim of this study is to develop and to validate a tool, which evaluates the quality of undergraduate medical educational websites; and apply it to the field of pathology. Methods: A tool was devised through several steps of item generation, reduction, weightage, pilot testing, post-pilot modification of the tool and validating the tool. Tool validation included measurement of inter-observer reliability; and generation of criterion related, construct related and content related validity. The validated tool was subsequently tested by applying it to a population of pathology websites. Results and Discussion: Reliability testing showed a high internal consistency reliability (Cronbach's alpha = 0.92), high inter-observer reliability (Pearson's correlation r = 0.88), intraclass correlation coefficient = 0.85 and &#954; =0.75. It showed high criterion related, construct related and content related validity. The tool showed moderately high concordance with the gold standard (&#954; =0.61); 92.2% sensitivity, 67.8% specificity, 75.6% positive predictive value and 88.9% negative predictive value. The validated tool was applied to 278 websites; 29.9% were rated as recommended, 41.0% as recommended with caution and 29.1% as not recommended. Conclusion: A systematic tool was devised to evaluate the quality of websites for medical educational purposes. The tool was shown to yield reliable and valid inferences through its application to pathology websites.
      Citation: Journal of Pathology Informatics 2013 4(1):29-29
      PubDate: Tue,29 Oct 2013
      DOI: 10.4103/2153-3539.120729
      Issue No: Vol. 4, No. 1 (2013)
       
  • Inter-reader variability in follicular lymphoma grading: Conventional and
           digital reading
    • Authors: Gerard Lozanski, Michael Pennell, Arwa Shana'ah, Weiqiang Zhao, Amy Gewirtz, Frederick Racke, Eric Hsi, Sabrina Simpson, Claudio Mosse, Shadia Alam, Sharon Swierczynski, Robert P Hasserjian, Metin N Gurcan
      Pages: 30 - 30
      Abstract: Gerard Lozanski, Michael Pennell, Arwa Shana'ah, Weiqiang Zhao, Amy Gewirtz, Frederick Racke, Eric Hsi, Sabrina Simpson, Claudio Mosse, Shadia Alam, Sharon Swierczynski, Robert P Hasserjian, Metin N Gurcan

      Journal of Pathology Informatics 2013 4(1):30-30

      Context: Pathologists grade follicular lymphoma (FL) cases by selecting 10, random high power fields (HPFs), counting the number of centroblasts (CBs) in these HPFs under the microscope and then calculating the average CB count for the whole slide. Previous studies have demonstrated that there is high inter-reader variability among pathologists using this methodology in grading. Aims: The objective of this study was to explore if newly available digital reading technologies can reduce inter-reader variability. Settings and Design: In this study, we considered three different reading conditions (RCs) in grading FL: (1) Conventional (glass-slide based) to establish the baseline, (2) digital whole slide viewing, (3) digital whole slide viewing with selected HPFs. Six board-certified pathologists from five different institutions read 17 FL slides in these three different RCs. Results: Although there was relative poor consensus in conventional reading, with lack of consensus in 41.2% of cases, which was similar to previously reported studies; we found that digital reading with pre-selected fields improved the inter-reader agreement, with only 5.9% lacking consensus among pathologists. Conclusions: Digital whole slide RC resulted in the worst concordance among pathologists while digital whole slide reading selected HPFs improved the concordance. Further studies are underway to determine if this performance can be sustained with a larger dataset and our automated HPF and CB detection algorithms can be employed to further improve the concordance.
      Citation: Journal of Pathology Informatics 2013 4(1):30-30
      PubDate: Tue,29 Oct 2013
      DOI: 10.4103/2153-3539.120747
      Issue No: Vol. 4, No. 1 (2013)
       
  • 3D prostate histology image reconstruction: Quantifying the impact of
           tissue deformation and histology section location
    • Authors: Eli Gibson, Mena Gaed, José A Gómez, Madeleine Moussa, Stephen Pautler, Joseph L Chin, Cathie Crukley, Glenn S Bauman, Aaron Fenster, Aaron D Ward
      Pages: 31 - 31
      Abstract: Eli Gibson, Mena Gaed, José A Gómez, Madeleine Moussa, Stephen Pautler, Joseph L Chin, Cathie Crukley, Glenn S Bauman, Aaron Fenster, Aaron D Ward

      Journal of Pathology Informatics 2013 4(1):31-31

      Background: Guidelines for localizing prostate cancer on imaging are ideally informed by registered post-prostatectomy histology. 3D histology reconstruction methods can support this by reintroducing 3D spatial information lost during histology processing. The need to register small, high-grade foci drives a need for high accuracy. Accurate 3D reconstruction method design is impacted by the answers to the following central questions of this work. (1) How does prostate tissue deform during histology processing? (2) What spatial misalignment of the tissue sections is induced by microtome cutting? (3) How does the choice of reconstruction model affect histology reconstruction accuracy? Materials and Methods: Histology, paraffin block face and magnetic resonance images were acquired for 18 whole mid-gland tissue slices from six prostates. 7-15 homologous landmarks were identified on each image. Tissue deformation due to histology processing was characterized using the target registration error (TRE) after landmark-based registration under four deformation models (rigid, similarity, affine and thin-plate-spline [TPS]). The misalignment of histology sections from the front faces of tissue slices was quantified using manually identified landmarks. The impact of reconstruction models on the TRE after landmark-based reconstruction was measured under eight reconstruction models comprising one of four deformation models with and without constraining histology images to the tissue slice front faces. Results: Isotropic scaling improved the mean TRE by 0.8-1.0 mm (all results reported as 95% confidence intervals), while skew or TPS deformation improved the mean TRE by
      Citation: Journal of Pathology Informatics 2013 4(1):31-31
      PubDate: Thu,31 Oct 2013
      Issue No: Vol. 4, No. 1 (2013)
       
  • Needs and workflow assessment prior to implementation of a digital
           pathology infrastructure for the US Air Force Medical Service
    • Authors: Jonhan Ho, Orly Aridor, David W Glinski, Christopher D Saylor, Joseph P Pelletier, Dale M Selby, Steven W Davis, Nicholas Lancia, Christopher B Gerlach, Jonathan Newberry, Leslie Anthony, Liron Pantanowitz, Anil V Parwani
      Pages: 32 - 32
      Abstract: Jonhan Ho, Orly Aridor, David W Glinski, Christopher D Saylor, Joseph P Pelletier, Dale M Selby, Steven W Davis, Nicholas Lancia, Christopher B Gerlach, Jonathan Newberry, Leslie Anthony, Liron Pantanowitz, Anil V Parwani

      Journal of Pathology Informatics 2013 4(1):32-32

      Background: Advances in digital pathology are accelerating integration of this technology into anatomic pathology (AP). To optimize implementation and adoption of digital pathology systems within a large healthcare organization, initial assessment of both end user (pathologist) needs and organizational infrastructure are required. Contextual inquiry is a qualitative, user-centered tool for collecting, interpreting, and aggregating such detailed data about work practices that can be employed to help identify specific needs and requirements. Aim: Using contextual inquiry, the objective of this study was to identify the unique work practices and requirements in AP for the United States (US) Air Force Medical Service (AFMS) that had to be targeted in order to support their transition to digital pathology. Subjects and Methods: A pathology-centered observer team conducted 1.5 h interviews with a total of 24 AFMS pathologists and histology lab personnel at three large regional centers and one smaller peripheral AFMS pathology center using contextual inquiry guidelines. Findings were documented as notes and arranged into a hierarchal organization of common themes based on user-provided data, defined as an affinity diagram. These data were also organized into consolidated graphic models that characterized AFMS pathology work practices, structure, and requirements. Results: Over 1,200 recorded notes were grouped into an affinity diagram composed of 27 third-level, 10 second-level, and five main-level (workflow and workload distribution, quality, communication, military culture, and technology) categories. When combined with workflow and cultural models, the findings revealed that AFMS pathologists had needs that were unique to their military setting, when compared to civilian pathologists. These unique needs included having to serve a globally distributed patient population, transient staff, but a uniform information technology (IT) structure. Conclusions: The contextual inquiry method helped reveal similarities and key differences with civilian pathologists. Such an analysis helped identify specific instances that would benefit from implementing digital pathology in a military environment. Employing digital pathology to facilitate workload distribution, secondary consultations, and quality assurance (over-reads) could help the AFMS deliver more accurate, efficient, and timely AP services at a global level.
      Citation: Journal of Pathology Informatics 2013 4(1):32-32
      PubDate: Fri,29 Nov 2013
      DOI: 10.4103/2153-3539.122388
      Issue No: Vol. 4, No. 1 (2013)
       
  • Laboratory informatics based evaluation of methylene tetrahydrofolate
           reductase C677T genetic test overutilization
    • Authors: David A Cohen, Brian H Shirts, Brian R Jackson, Lisa S Parker
      Pages: 33 - 33
      Abstract: David A Cohen, Brian H Shirts, Brian R Jackson, Lisa S Parker

      Journal of Pathology Informatics 2013 4(1):33-33

      Background: Laboratory data can provide a wide range of information to estimate adherence to guidelines and proper utilization of genetic testing. The methylene tetrahydrofolate reductase (MTHFR) C677T variant has been demonstrated to have negligible utility in patient management. However, the testing of this variant remains pervasive. The purpose of this study was to develop methods to analyze concordance of clinician ordering practices with national guidelines. Methods: We used laboratory data to extract specific data elements including patient demographics, timestamps, physician ordering logs and temporal relationship to chemistry requests to examine 245 consecutive MTHFR tests ordered in 2011 at an academic tertiary center. A comprehensive chart review was used to identify indications for testing. These results were correlated with a retrospective analysis of 4,226 tests drawn at a range of hospitals requesting testing from a national reference laboratory over a 2-year period. MTHFR ordering practices drawn from 17 institutions were examined longitudinally from 2002 to 2011. Results: Indications for testing included cerebrovascular events (40.0%) and venous thrombosis (39.1%). Family history prompted testing in eight cases. Based on acceptable hypercoagulability guidelines recommending MTHFR C677T testing only in the presence of elevated serum homocysteine, 10.6% (22/207) of adult patients met an indicated threshold at an academic tertiary center. Among 77 institutions, 14.5% (613/4226) of MTHFR testing met recommendations. Conclusion: We demonstrate an effective method to examine discreet elements of a molecular diagnostics laboratory information system at a tertiary care institution and to correlate these findings at a national level. Retrospective examination of clinicians' request of MTHFR C677T genetic testing strongly suggests that clinicians have failed to adjust their ordering practices in light of evolving scientific and professional organization recommendations.
      Citation: Journal of Pathology Informatics 2013 4(1):33-33
      PubDate: Fri,29 Nov 2013
      DOI: 10.4103/2153-3539.122389
      Issue No: Vol. 4, No. 1 (2013)
       
  • Applying perceptual and adaptive learning techniques for teaching
           introductory histopathology
    • Authors: Sally Krasne, Joseph D Hillman, Philip J Kellman, Thomas A Drake
      Pages: 34 - 34
      Abstract: Sally Krasne, Joseph D Hillman, Philip J Kellman, Thomas A Drake

      Journal of Pathology Informatics 2013 4(1):34-34

      Background: Medical students are expected to master the ability to interpret histopathologic images, a difficult and time-consuming process. A major problem is the issue of transferring information learned from one example of a particular pathology to a new example. Recent advances in cognitive science have identified new approaches to address this problem. Methods: We adapted a new approach for enhancing pattern recognition of basic pathologic processes in skin histopathology images that utilizes perceptual learning techniques, allowing learners to see relevant structure in novel cases along with adaptive learning algorithms that space and sequence different categories (e.g. diagnoses) that appear during a learning session based on each learner's accuracy and response time (RT). We developed a perceptual and adaptive learning module (PALM) that utilized 261 unique images of cell injury, inflammation, neoplasia, or normal histology at low and high magnification. Accuracy and RT were tracked and integrated into a "Score" that reflected students rapid recognition of the pathologies and pre- and post-tests were given to assess the effectiveness. Results: Accuracy, RT and Scores significantly improved from the pre- to post-test with Scores showing much greater improvement than accuracy alone. Delayed post-tests with previously unseen cases, given after 6-7 weeks, showed a decline in accuracy relative to the post-test for 1 st -year students, but not significantly so for 2 nd -year students. However, the delayed post-test scores maintained a significant and large improvement relative to those of the pre-test for both 1 st and 2 nd year students suggesting good retention of pattern recognition. Student evaluations were very favorable. Conclusion: A web-based learning module based on the principles of cognitive science showed an evidence for improved recognition of histopathology patterns by medical students.
      Citation: Journal of Pathology Informatics 2013 4(1):34-34
      PubDate: Tue,31 Dec 2013
      DOI: 10.4103/2153-3539.123991
      Issue No: Vol. 4, No. 1 (2013)
       
  • Computational analysis of p63 + nuclei distribution pattern by
           graph theoretic approach in an oral pre-cancer (sub-mucous fibrosis)
    • Authors: Swarnendu Bag, Sailesh Conjeti, Raunak Kumar Das, Mousami Pal, Anji Anura, Ranjan Rashmi Paul, Ajoy Kumar Ray, Sanghamitra Sengupta, Jyotirmoy Chatterjee
      Pages: 35 - 35
      Abstract: Swarnendu Bag, Sailesh Conjeti, Raunak Kumar Das, Mousami Pal, Anji Anura, Ranjan Rashmi Paul, Ajoy Kumar Ray, Sanghamitra Sengupta, Jyotirmoy Chatterjee

      Journal of Pathology Informatics 2013 4(1):35-35

      Background: Oral submucous fibrosis (OSF) is a pre-cancerous condition with features of chronic, inflammatory and progressive sub-epithelial fibrotic disorder of the buccal mucosa. In this study, malignant potentiality of OSF has been assessed by quantification of immunohistochemical expression of epithelial prime regulator-p63 molecule in correlation to its malignant (oral squamous cell carcinoma [OSCC] and normal counterpart [normal oral mucosa [NOM]). Attributes of spatial extent and distribution of p63 + expression in the epithelium have been investigated. Further, a correlated assessment of histopathological attributes inferred from H&E staining and their mathematical counterparts (molecular pathology of p63) have been proposed. The suggested analytical framework envisaged standardization of the immunohistochemistry evaluation procedure for the molecular marker, using computer-aided image analysis, toward enhancing its prognostic value. Subjects and Methods: In histopathologically confirmed OSF, OSCC and NOM tissue sections, p63 + nuclei were localized and segmented by identifying regional maxima in plateau-like intensity spatial profiles of nuclei. The clustered nuclei were localized and segmented by identifying concave points in the morphometry and by marker-controlled watersheds. Voronoi tessellations were constructed around nuclei centroids and mean values of spatial-relation metrics such as tessellation area, tessellation perimeter, roundness factor and disorder of the area were extracted. Morphology and extent of expression are characterized by area, diameter, perimeter, compactness, eccentricity and density, fraction of p63 + expression and expression distance of p63 + nuclei. Results: Correlative framework between histopathological features characterizing malignant potentiality and their quantitative p63 counterparts was developed. Statistical analyses of mathematical trends were evaluated between different biologically relevant combinations: (i) NOM to oral submucous fibrosis without dysplasia (OSFWT) (ii) NOM to oral submucous fibrosis with dysplasia (OSFWD) (iii) OSFWT-OSFWD (iv) OSFWD-OSCC. Significant histopathogical correlates and their corroborative mathematical features, inferred from p63 staining, were also investigated into. Conclusion: Quantitative assessment and correlative analysis identified mathematical features related to hyperplasia, cellular stratification, differentiation and maturation, shape and size, nuclear crowding and nucleocytoplasmic ratio. It is envisaged that this approach for analyzing the p63 expression and its distribution pattern may help to establish it as a quantitative bio-marker to predict the malignant potentiality and progression. The proposed work would be a value addition to the gold standard by incorporating an observer-independent framework for the associated molecular pathology.
      Citation: Journal of Pathology Informatics 2013 4(1):35-35
      PubDate: Tue,31 Dec 2013
      DOI: 10.4103/2153-3539.124006
      Issue No: Vol. 4, No. 1 (2013)
       
  • Color correction for automatic fibrosis quantification in liver biopsy
           specimens
    • Authors: Yuri Murakami, Tokiya Abe, Akinori Hashiguchi, Masahiro Yamaguchi, Akira Saito, Michiie Sakamoto
      Pages: 36 - 36
      Abstract: Yuri Murakami, Tokiya Abe, Akinori Hashiguchi, Masahiro Yamaguchi, Akira Saito, Michiie Sakamoto

      Journal of Pathology Informatics 2013 4(1):36-36

      Context: For a precise and objective quantification of liver fibrosis, quantitative evaluations through image analysis have been utilized. However, manual operations are required in most cases for extracting fiber areas because of color variation included in digital pathology images. Aims: The purpose of this research is to propose a color correction method for whole slide images (WSIs) of Elastica van Gieson (EVG) stained liver biopsy tissue specimens and to realize automated operation of image analysis for fibrosis quantification. Materials and Methods: Our experimental dataset consisted of 38 WSIs of liver biopsy specimens collected from 38 chronic viral hepatitis patients from multiple medical facilities, stained with EVG and scanned at &#215;20 using a Nano Zoomer 2.0 HT (Hamamatsu Photonics K.K., Hamamatsu, Japan). Color correction was performed by modifying the color distribution of a target WSI so as to fit to the reference, where the color distribution was modeled by a set of two triangle pyramids. Using color corrected WSIs; fibrosis quantification was performed based on tissue classification analysis. Statistical Analysis Used: Spearman's rank correlation coefficients were calculated between liver stiffness measured by transient elastography and median area ratio of collagen fibers calculated based on tissue classification results. Results: Statistical analysis results showed a significant correlation r = 0.61-0.68 even when tissue classifiers were trained by using a subset of WSIs, while the correlation coefficients were reduced to r = 0.40-0.50 without color correction. Conclusions: Fibrosis quantification accompanied with the proposed color correction method could provide an objective evaluation tool for liver fibrosis, which complements semi-quantitative histologic evaluation systems.
      Citation: Journal of Pathology Informatics 2013 4(1):36-36
      PubDate: Tue,31 Dec 2013
      DOI: 10.4103/2153-3539.124009
      Issue No: Vol. 4, No. 1 (2013)
       
  • Needs and workflow assessment prior to implementation of a digital
           pathology infrastructure for the US Air Force Medical Service
    • Authors: Keith J Kaplan
      Pages: 37 - 37
      Abstract: Keith J Kaplan

      Journal of Pathology Informatics 2013 4(1):37-37


      Citation: Journal of Pathology Informatics 2013 4(1):37-37
      PubDate: Tue,31 Dec 2013
      Issue No: Vol. 4, No. 1 (2013)
       
  • Optimal z-axis scanning parameters for gynecologic cytology specimens
    • Authors: Amber D Donnelly, Maheswari S Mukherjee, Elizabeth R Lyden, Julia A Bridge, Subodh M Lele, Najia Wright, Mary F McGaughey, Alicia M Culberson, Adam J Horn, Whitney R Wedel, Stanley J Radio
      Pages: 38 - 38
      Abstract: Amber D Donnelly, Maheswari S Mukherjee, Elizabeth R Lyden, Julia A Bridge, Subodh M Lele, Najia Wright, Mary F McGaughey, Alicia M Culberson, Adam J Horn, Whitney R Wedel, Stanley J Radio

      Journal of Pathology Informatics 2013 4(1):38-38

      Background: The use of virtual microscopy (VM) in clinical cytology has been limited due to the inability to focus through three dimensional (3D) cell clusters with a single focal plane (2D images). Limited information exists regarding the optimal scanning parameters for 3D scanning. Aims: The purpose of this study was to determine the optimal number of the focal plane levels and the optimal scanning interval to digitize gynecological (GYN) specimens prepared on SurePath&#8482; glass slides while maintaining a manageable file size. Subjects and Methods: The iScanCoreo Au scanner (Ventana, AZ, USA) was used to digitize 192 SurePath&#8482; glass slides at three focal plane levels at 1 &#956; interval. The digitized virtual images (VI) were annotated using BioImagene's Image Viewer. Five participants interpreted the VI and recorded the focal plane level at which they felt confident and later interpreted the corresponding glass slide specimens using light microscopy (LM). The participants completed a survey about their experiences. Inter-rater agreement and concordance between the VI and the glass slide specimens were evaluated. Results: This study determined an overall high intra-rater diagnostic concordance between glass and VI (89-97%), however, the inter-rater agreement for all cases was higher for LM (94%) compared with VM (82%). Survey results indicate participants found low grade dysplasia and koilocytes easy to diagnose using three focal plane levels, the image enhancement tool was useful and focusing through the cells helped with interpretation; however, the participants found VI with hyperchromatic crowded groups challenging to interpret. Participants reported they prefer using LM over VM. This study supports using three focal plane levels and 1 &#956; interval to expand the use of VM in GYN cytology. Conclusion: Future improvements in technology and appropriate training should make this format a more preferable and practical option in clinical cytology.
      Citation: Journal of Pathology Informatics 2013 4(1):38-38
      PubDate: Tue,31 Dec 2013
      DOI: 10.4103/2153-3539.124015
      Issue No: Vol. 4, No. 1 (2013)
       
  • A pathologist-in-the-loop IHC antibody test selection using the
           entropy-based probabilistic method
    • Authors: Dmitriy Shin, Gerald Arthur, Charles Caldwell, Mihail Popescu, Marius Petruc, Alberto Diaz-Arias, Chi-Ren Shyu
      Pages: 1 - 1
      Abstract: Dmitriy Shin, Gerald Arthur, Charles Caldwell, Mihail Popescu, Marius Petruc, Alberto Diaz-Arias, Chi-Ren Shyu

      Journal of Pathology Informatics 2012 3(1):1-1

      Background: Immunohistochemistry (IHC) is an important tool to identify and quantify expression of certain proteins (antigens) to gain insights into the molecular processes in a diseased tissue. However, it is a challenge for pathologists to remember the discriminative characteristics of the growing number of such antigens across multiple diseases. The complexity of their expression patterns, fueled by continuous discoveries in molecular pathology, gives rise to a combinatorial explosion that places an unprecedented burden on a practicing pathologist and therefore increases cost and variability of IHC studies. Materials and Methods: To tackle these issues, we have developed antibody test optimized selection method, a novel informatics tool to help pathologists in improving the IHC antibody selection process. The method uses extensions of Shannon's information entropies and Bayesian probabilities to dynamically build an efficient diagnostic tree. Results: A comparative analysis of our method with the expert and World Health Organization classification guidelines showed that the proposed method brings threefold reduction in number of antibody tests required to reach a diagnostic conclusion. Conclusion: The developed method can significantly streamline the antibody test selection process, decrease associated costs and reduce inter- and intrapathologist variability in IHC decision-making.
      Citation: Journal of Pathology Informatics 2012 3(1):1-1
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93393
      Issue No: Vol. 3, No. 1 (2012)
       
  • Virtual microscopy using whole-slide imaging as an enabler for
           teledermatopathology: A paired consultant validation study
    • Authors: Ayman Al Habeeb, Andrew Evans, Danny Ghazarian
      Pages: 2 - 2
      Abstract: Ayman Al Habeeb, Andrew Evans, Danny Ghazarian

      Journal of Pathology Informatics 2012 3(1):2-2

      Background: There is a need for telemedicine, particularly in countries with large geographical areas and widely scattered low-density communities as is the case of the Canadian system, particularly if equality of care is to be achieved or the difference gap is to be narrowed between urban centers and more peripheral communities. Aims: 1. To validate teledermatopathology as a diagnostic tool in under-serviced areas; 2. To test its utilization in inflammatory and melanocytic lesions; 3. To compare the impact of 20&#215; (0.5 &#956;m/pixel) and 40&#215; (0.25 &#956;m/pixel) scans on the diagnostic accuracy. Materials and Methods: A total of 103 dermatopathology cases divided into three arms were evaluated by two pathologists and results compared. The first arm consisted of 79 consecutive routine cases (n=79). The second arm consisted of 12 inflammatory skin biopsies (n=12) and the third arm consisted of 12 melanocytic lesions (n=12). Diagnosis concordance was used to evaluate the first arm. Whereas concordance of preset objective findings were used to evaluate the second and third arms. Results: The diagnostic concordance rate for the first arm was 96%. The concordance rates of the objective findings for the second and third arms were 100%. The image quality was deemed superior to light microscopy for 40&#215; scans. Conclusion: The current scanners produce high-resolution images that are adequate for evaluation of a variety of cases of different complexities.
      Citation: Journal of Pathology Informatics 2012 3(1):2-2
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93399
      Issue No: Vol. 3, No. 1 (2012)
       
  • A novel strategy for evaluating the effects of an electronic test ordering
           alert message: Optimizing cardiac marker use
    • Authors: Jason M Baron, Kent B Lewandrowski, Irina K Kamis, Balaji Singh, Sidi M Belkziz, Anand S Dighe
      Pages: 3 - 3
      Abstract: Jason M Baron, Kent B Lewandrowski, Irina K Kamis, Balaji Singh, Sidi M Belkziz, Anand S Dighe

      Journal of Pathology Informatics 2012 3(1):3-3

      Background: Laboratory ordering functions within computerized provider order entry (CPOE) systems typically support the display of electronic alert messages to improve test utilization or implement new ordering policies. However, alert strategies have been shown to vary considerably in their success and the characteristics contributing to an alert's success are poorly understood. Improved methodologies are needed to evaluate alerts and their mechanisms of action. Materials and Methods: Clinicians order inpatient and emergency department laboratory tests using our institutional CPOE system. We analyzed user interaction data captured by our CPOE system to evaluate how clinicians responded to an alert. We evaluated an alert designed to implement an institutional policy restricting the indications for ordering creatine kinase-MB (CKMB). Results: Within 2 months of alert implementation, CKMB-associated searches declined by 79% with a corresponding decline in CKMB orders. Furthermore, while prior to alert implementation, clinicians searching for CKMB ultimately ordered this test 99% of the time, following implementation, only 60% of CKMB searches ultimately led to CKMB test orders. This difference presumably represents clinicians who reconsidered the need for CKMB in response to the alert, demonstrating the alert's just-in-time advisory capability. In addition, as clinicians repeatedly viewed the alert, there was a "dose-dependant" decrease in the fraction of searches without orders. This presumably reflects the alerting strategy's long-term educational component, as clinicians aware of the new policy will not search for CKMB when not indicated. Conclusions: Our analytic approach provides insight into the mechanism of a CPOE alert and demonstrates that alerts may act through a combination of just-in-time advice and longer term education. Use of this approach when implementing alerts may prove useful to improve the success of a given alerting strategy.
      Citation: Journal of Pathology Informatics 2012 3(1):3-3
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93400
      Issue No: Vol. 3, No. 1 (2012)
       
  • Full field optical coherence tomography can identify spermatogenesis in a
           rodent sertoli-cell only model
    • Authors: Ranjith Ramasamy, Joshua Sterling, Maryem Manzoor, Bekheit Salamoon, Manu Jain, Erik Fisher, Phillip S Li, Peter N Schlegel, Sushmita Mukherjee
      Pages: 4 - 4
      Abstract: Ranjith Ramasamy, Joshua Sterling, Maryem Manzoor, Bekheit Salamoon, Manu Jain, Erik Fisher, Phillip S Li, Peter N Schlegel, Sushmita Mukherjee

      Journal of Pathology Informatics 2012 3(1):4-4

      Background: Microdissection testicular sperm extraction (micro-TESE) has replaced conventional testis biopsies as a method of choice for obtaining sperm for in vitro fertilization for men with nonobstructive azoospermia. A technical challenge of micro-TESE is that the low magnification inspection of the tubules with a surgical microscope is insufficient to definitively identify sperm-containing tubules, necessitating tissue removal and cytologic assessment. Full field optical coherence tomography (FFOCT) uses white light interference microscopy to generate quick high-resolution tomographic images of fresh (unprocessed and unstained) tissue. Furthermore, by using a nonlaser safe light source (150 W halogen lamp) for tissue illumination, it ensures that the sperm extracted for in vitro fertilization are not photo-damaged or mutagenized. Materials and Methods: A focal Sertoli-cell only rodent model was created with busulfan injection in adult rats. Ex vivo testicular tissues from both normal and busulfan-treated rats were imaged with a commercial modified FFOCT system, Light-CT TM , and the images were correlated with gold standard hematoxylin and eosin staining. Results: Light-CT TM identified spermatogenesis within the seminiferous tubules in freshly excised testicular tissue, without the use of exogenous contrast or fixation. Normal adult rats exhibited tubules with uniform size and shape (diameter 328 &#177;11 &#956;m). The busulfan-treated animals showed marked heterogeneity in tubular size and shape (diameter 178 &#177; 35 &#956;m) and only 10% contained sperm within the lumen. Conclusion : FFOCT has the potential to facilitate real-time visualization of spermatogenesis in humans, and aid in micro-TESE for men with infertility.
      Citation: Journal of Pathology Informatics 2012 3(1):4-4
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93401
      Issue No: Vol. 3, No. 1 (2012)
       
  • How useful are delta checks in the 21st century? A
           stochastic-dynamic model of specimen mix-up and detection
    • Authors: Katie Ovens, Christopher Naugler
      Pages: 5 - 5
      Abstract: Katie Ovens, Christopher Naugler

      Journal of Pathology Informatics 2012 3(1):5-5

      Introduction: Delta checks use two specimen test results taken in succession in order to detect test result changes greater than expected physiological variation. One of the most common and serious errors detected by delta checks is specimen mix-up errors. The positive and negative predictive values of delta checks for detecting specimen mix-up errors, however, are largely unknown. Materials and Methods: We addressed this question by first constructing a stochastic dynamic model using repeat test values for five analytes from approximately 8000 inpatients in Calgary, Alberta, Canada. The analytes examined were sodium, potassium, chloride, bicarbonate, and creatinine. The model simulated specimen mix-up errors by randomly switching a set number of pairs of second test results. Sensitivities and specificities were then calculated for each analyte for six combinations of delta check equations and cut-off values from the published literature. Results: Delta check specificities obtained from this model ranged from 50% to 99%; however the sensitivities were generally below 20% with the exception of creatinine for which the best performing delta check had a sensitivity of 82.8%. Within a plausible incidence range of specimen mix-ups the positive predictive values of even the best performing delta check equation and analyte became negligible. Conclusion: This finding casts doubt on the ongoing clinical utility of delta checks in the setting of low rates of specimen mix-ups.
      Citation: Journal of Pathology Informatics 2012 3(1):5-5
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93402
      Issue No: Vol. 3, No. 1 (2012)
       
  • All aboard: Cytotechnology student training in pathology informatics
    • Authors: Judith Modery, Walid E Khalbuss, Liron Pantanowitz
      Pages: 6 - 6
      Abstract: Judith Modery, Walid E Khalbuss, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):6-6


      Citation: Journal of Pathology Informatics 2012 3(1):6-6
      PubDate: Wed,29 Feb 2012
      DOI: 10.4103/2153-3539.93403
      Issue No: Vol. 3, No. 1 (2012)
       
  • Review of "Informatics in Medical Imaging" by Kagadis GC, Langer
           SG (Editors)
    • Authors: Claudia Mello-Thoms
      Pages: 7 - 7
      Abstract: Claudia Mello-Thoms

      Journal of Pathology Informatics 2012 3(1):7-7


      Citation: Journal of Pathology Informatics 2012 3(1):7-7
      PubDate: Wed,29 Feb 2012
      Issue No: Vol. 3, No. 1 (2012)
       
  • Tryggo: Old norse for truth - The real truth about ground truth: New
           insights into the challenges of generating ground truth maps for WSI CAD
           algorithm evaluation
    • Authors: Jason D Hipp, Steven C Smith, Jeffrey Sica, David Lucas, Jennifer A Hipp, Lakshmi P Kunju, Ulysses J Balis
      Pages: 8 - 8
      Abstract: Jason D Hipp, Steven C Smith, Jeffrey Sica, David Lucas, Jennifer A Hipp, Lakshmi P Kunju, Ulysses J Balis

      Journal of Pathology Informatics 2012 3(1):8-8


      Citation: Journal of Pathology Informatics 2012 3(1):8-8
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93890
      Issue No: Vol. 3, No. 1 (2012)
       
  • Referenceless image quality evaluation for whole slide imaging
    • Authors: Noriaki Hashimoto, Pinky A Bautista, Masahiro Yamaguchi, Nagaaki Ohyama, Yukako Yagi
      Pages: 9 - 9
      Abstract: Noriaki Hashimoto, Pinky A Bautista, Masahiro Yamaguchi, Nagaaki Ohyama, Yukako Yagi

      Journal of Pathology Informatics 2012 3(1):9-9

      Objective: The image quality in whole slide imaging (WSI) is one of the most important issues for the practical use of WSI scanners. In this paper, we proposed an image quality evaluation method for scanned slide images in which no reference image is required. Methods: While most of the conventional methods for no-reference evaluation only deal with one image degradation at a time, the proposed method is capable of assessing both blur and noise by using an evaluation index which is calculated using the sharpness and noise information of the images in a given training data set by linear regression analysis. The linear regression coefficients can be determined in two ways depending on the purpose of the evaluation. For objective quality evaluation, the coefficients are determined using a reference image with mean square error as the objective value in the analysis. On the other hand, for subjective quality evaluation, the subjective scores given by human observers are used as the objective values in the analysis. The predictive linear regression models for the objective and subjective image quality evaluations, which were constructed using training images, were then used on test data wherein the calculated objective values are construed as the evaluation indices. Results: The results of our experiments confirmed the effectiveness of the proposed image quality evaluation method in both objective and subjective image quality measurements. Finally, we demonstrated the application of the proposed evaluation method to the WSI image quality assessment and automatic rescanning in the WSI scanner.
      Citation: Journal of Pathology Informatics 2012 3(1):9-9
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93891
      Issue No: Vol. 3, No. 1 (2012)
       
  • Integration of digital gross pathology images for enterprise-wide access
    • Authors: Milon Amin, Gaurav Sharma, Anil V Parwani, Ralph Anderson, Brian J Kolowitz, Anthony Piccoli, Rasu B Shrestha, Gonzalo Romero Lauro, Liron Pantanowitz
      Pages: 10 - 10
      Abstract: Milon Amin, Gaurav Sharma, Anil V Parwani, Ralph Anderson, Brian J Kolowitz, Anthony Piccoli, Rasu B Shrestha, Gonzalo Romero Lauro, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):10-10

      Background: Sharing digital pathology images for enterprise- wide use into a picture archiving and communication system (PACS) is not yet widely adopted. We share our solution and 3-year experience of transmitting such images to an enterprise image server (EIS). Methods: Gross pathology images acquired by prosectors were integrated with clinical cases into the laboratory information system's image management module, and stored in JPEG2000 format on a networked image server. Automated daily searches for cases with gross images were used to compile an ASCII text file that was forwarded to a separate institutional Enterprise Digital Imaging and Communications in Medicine (DICOM) Wrapper (EDW) server. Concurrently, an HL7-based image order for these cases was generated, containing the locations of images and patient data, and forwarded to the EDW, which combined data in these locations to generate images with patient data, as required by DICOM standards. The image and data were then "wrapped" according to DICOM standards, transferred to the PACS servers, and made accessible on an institution-wide basis. Results: In total, 26,966 gross images from 9,733 cases were transmitted over the 3-year period from the laboratory information system to the EIS. The average process time for cases with successful automatic uploads (n=9,688) to the EIS was 98 seconds. Only 45 cases (0.5%) failed requiring manual intervention. Uploaded images were immediately available to institution- wide PACS users. Since inception, user feedback has been positive. Conclusions: Enterprise- wide PACS- based sharing of pathology images is feasible, provides useful services to clinical staff, and utilizes existing information system and telecommunications infrastructure. PACS-shared pathology images, however, require a "DICOM wrapper" for multisystem compatibility.
      Citation: Journal of Pathology Informatics 2012 3(1):10-10
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93892
      Issue No: Vol. 3, No. 1 (2012)
       
  • Clinical fellowship training in pathology informatics: A program
           description
    • Authors: John R Gilbertson, David S McClintock, Roy E Lee, Maristela Onozato, Frank C Kuo, Bruce A Beckwith, Yukako Yagi, Anand S Dighe, Tom M Gudewicz, Long P Le, David C Wilbur, Ji Yeon Kim, Victor B Brodsky, Stephen Black-Schaffer
      Pages: 11 - 11
      Abstract: John R Gilbertson, David S McClintock, Roy E Lee, Maristela Onozato, Frank C Kuo, Bruce A Beckwith, Yukako Yagi, Anand S Dighe, Tom M Gudewicz, Long P Le, David C Wilbur, Ji Yeon Kim, Victor B Brodsky, Stephen Black-Schaffer

      Journal of Pathology Informatics 2012 3(1):11-11

      Background: In 2007, our healthcare system established a clinical fellowship program in pathology informatics. In 2011, the program benchmarked its structure and operations against a 2009 white paper "Program requirements for fellowship education in the subspecialty of clinical informatics," endorsed by the Board of the American Medical Informatics Association (AMIA) that described a proposal for a general clinical informatics fellowship program. Methods: A group of program faculty members and fellows compared each of the proposed requirements in the white paper with the fellowship program's written charter and operations. The majority of white paper proposals aligned closely with the rules and activities in our program and comparison was straightforward. In some proposals, however, differences in terminology, approach, and philosophy made comparison less direct, and in those cases, the thinking of the group was recorded. After the initial evaluation, the remainder of the faculty reviewed the results and any disagreements were resolved. Results: The most important finding of the study was how closely the white paper proposals for a general clinical informatics fellowship program aligned with the reality of our existing pathology informatics fellowship. The program charter and operations of the program were judged to be concordant with the great majority of specific white paper proposals. However, there were some areas of discrepancy and the reasons for the discrepancies are discussed in the manuscript. Conclusions: After the comparison, we conclude that the existing pathology informatics fellowship could easily meet all substantive proposals put forth in the 2009 clinical informatics program requirements white paper. There was also agreement on a number of philosophical issues, such as the advantages of multiple fellows, the need for core knowledge and skill sets, and the need to maintain clinical skills during informatics training. However, there were other issues, such as a requirement for a 2-year fellowship and for informatics fellowships to be done after primary board certification, that pathology should consider carefully as it moves toward a subspecialty status and board certification.
      Citation: Journal of Pathology Informatics 2012 3(1):11-11
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93893
      Issue No: Vol. 3, No. 1 (2012)
       
  • Board certification for pathologists in clinical informatics: Are you a
           lumper or a splitter?
    • Authors: Alexis B Carter
      Pages: 12 - 12
      Abstract: Alexis B Carter

      Journal of Pathology Informatics 2012 3(1):12-12


      Citation: Journal of Pathology Informatics 2012 3(1):12-12
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93894
      Issue No: Vol. 3, No. 1 (2012)
       
  • Isolation and two-step classification of normal white blood cells in
           peripheral blood smears
    • Authors: Nisha Ramesh, Bryan Dangott, Mohammed E Salama, Tolga Tasdizen
      Pages: 13 - 13
      Abstract: Nisha Ramesh, Bryan Dangott, Mohammed E Salama, Tolga Tasdizen

      Journal of Pathology Informatics 2012 3(1):13-13

      Introduction: An automated system for differential white blood cell (WBC) counting based on morphology can make manual differential leukocyte counts faster and less tedious for pathologists and laboratory professionals. We present an automated system for isolation and classification of WBCs in manually prepared, Wright stained, peripheral blood smears from whole slide images (WSI). Methods: A simple, classification scheme using color information and morphology is proposed. The performance of the algorithm was evaluated by comparing our proposed method with a hematopathologist's visual classification. The isolation algorithm was applied to 1938 subimages of WBCs, 1804 of them were accurately isolated. Then, as the first step of a two-step classification process, WBCs were broadly classified into cells with segmented nuclei and cells with nonsegmented nuclei. The nucleus shape is one of the key factors in deciding how to classify WBCs. Ambiguities associated with connected nuclear lobes are resolved by detecting maximum curvature points and partitioning them using geometric rules. The second step is to define a set of features using the information from the cytoplasm and nuclear regions to classify WBCs using linear discriminant analysis. This two-step classification approach stratifies normal WBC types accurately from a whole slide image. Results: System evaluation is performed using a 10-fold cross-validation technique. Confusion matrix of the classifier is presented to evaluate the accuracy for each type of WBC detection. Experiments show that the two-step classification implemented achieves a 93.9% overall accuracy in the five subtype classification. Conclusion: Our methodology achieves a semiautomated system for the detection and classification of normal WBCs from scanned WSI. Further studies will be focused on detecting and segmenting abnormal WBCs, comparison of 20&#215; and 40&#215; data, and expanding the applications for bone marrow aspirates.
      Citation: Journal of Pathology Informatics 2012 3(1):13-13
      PubDate: Fri,16 Mar 2012
      DOI: 10.4103/2153-3539.93895
      Issue No: Vol. 3, No. 1 (2012)
       
  • Comment on "Quality evaluation of microscopy and scanned histological
           images for diagnostic purposes": Are scanners better than
           microscopes?
    • Authors: Yukako Yagi, Liron Pantanowitz
      Pages: 14 - 14
      Abstract: Yukako Yagi, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):14-14


      Citation: Journal of Pathology Informatics 2012 3(1):14-14
      PubDate: Wed,18 Apr 2012
      Issue No: Vol. 3, No. 1 (2012)
       
  • Handheld computing in pathology
    • Authors: Seung Park, Anil Parwani, Mahadev Satyanarayanan, Liron Pantanowitz
      Pages: 15 - 15
      Abstract: Seung Park, Anil Parwani, Mahadev Satyanarayanan, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):15-15

      Handheld computing has had many applications in medicine, but relatively few in pathology. Most reported uses of handhelds in pathology have been limited to experimental endeavors in telemedicine or education. With recent advances in handheld hardware and software, along with concurrent advances in whole-slide imaging (WSI), new opportunities and challenges have presented themselves. This review addresses the current state of handheld hardware and software, provides a history of handheld devices in medicine focusing on pathology, and presents future use cases for such handhelds in pathology.
      Citation: Journal of Pathology Informatics 2012 3(1):15-15
      PubDate: Wed,18 Apr 2012
      DOI: 10.4103/2153-3539.95127
      Issue No: Vol. 3, No. 1 (2012)
       
  • Changes, disruption and innovation: An investigation of the introduction
           of new health information technology in a microbiology laboratory
    • Authors: George Toouli, Andrew Georgiou, Johanna Westbrook
      Pages: 16 - 16
      Abstract: George Toouli, Andrew Georgiou, Johanna Westbrook

      Journal of Pathology Informatics 2012 3(1):16-16

      Background: It is expected that health information technology (HIT) will deliver a safer, more efficient and effective health care system. The aim of this study was to undertake a qualitative and video-ethnographic examination of the impact of information technologies on work processes in the reception area of a Microbiology Department, to ascertain what changed, how it changed and the impact of the change. Materials and Methods: The setting for this study was the microbiology laboratory of a large tertiary hospital in Sydney. The study consisted of qualitative (interview and focus group) data and observation sessions for the period August 2005 to October 2006 along with video footage shot in three sessions covering the original system and the two stages of the Cerner implementation. Data analysis was assisted by NVivo software and process maps were produced from the video footage. Results: There were two laboratory information systems observed in the video footage with computerized provider order entry introduced four months later. Process maps highlighted the large number of pre data entry steps with the original system whilst the newer system incorporated many of these steps in to the data entry stage. However, any time saved with the new system was offset by the requirement to complete some data entry of patient information not previously required. Other changes noted included the change of responsibilities for the reception staff and the physical changes required to accommodate the increased activity around the data entry area. Conclusions: Implementing a new HIT is always an exciting time for any environment but ensuring that the implementation goes smoothly and with minimal trouble requires the administrator and their team to plan well in advance for staff training, physical layout and possible staff resource reallocation.
      Citation: Journal of Pathology Informatics 2012 3(1):16-16
      PubDate: Wed,18 Apr 2012
      DOI: 10.4103/2153-3539.95128
      Issue No: Vol. 3, No. 1 (2012)
       
  • Compressing pathology whole-slide images using a human and model observer
           evaluation
    • Authors: Elizabeth A Krupinski, Jeffrey P Johnson, Stacey Jaw, Anna R Graham, Ronald S Weinstein
      Pages: 17 - 17
      Abstract: Elizabeth A Krupinski, Jeffrey P Johnson, Stacey Jaw, Anna R Graham, Ronald S Weinstein

      Journal of Pathology Informatics 2012 3(1):17-17

      Introduction: We aim to determine to what degree whole-slide images (WSI) can be compressed without impacting the ability of the pathologist to distinguish benign from malignant tissues. An underlying goal is to demonstrate the utility of a visual discrimination model (VDM) for predicting observer performance. Materials and Methods: A total of 100 regions of interest (ROIs) from a breast biopsy whole-slide images at five levels of JPEG 2000 compression (8:1, 16:1, 32:1, 64:1, and 128:1) plus the uncompressed version were shown to six pathologists to determine benign versus malignant status. Results: There was a significant decrease in performance as a function of compression ratio (F = 14.58, P < 0.0001). The visibility of compression artifacts in the test images was predicted using a VDM. Just-noticeable difference (JND) metrics were computed for each image, including the mean, median, &#8805;90th percentiles, and maximum values. For comparison, PSNR (peak signal-to-noise ratio) and Structural Similarity (SSIM) were also computed. Image distortion metrics were computed as a function of compression ratio and averaged across test images. All of the JND metrics were found to be highly correlated and differed primarily in magnitude. Both PSNR and SSIM decreased with bit rate, correctly reflecting a loss of image fidelity with increasing compression. Observer performance as measured by the Receiver Operating Characteristic area under the curve (ROC Az) was nearly constant up to a compression ratio of 32:1, then decreased significantly for 64:1 and 128:1 compression levels. The initial decline in Az occurred around a mean JND of 3, Minkowski JND of 4, and 99th percentile JND of 6.5. Conclusion: Whole-slide images may be compressible to relatively high levels before impacting WSI interpretation performance. The VDM metrics correlated well with artifact conspicuity and human performance.
      Citation: Journal of Pathology Informatics 2012 3(1):17-17
      PubDate: Wed,18 Apr 2012
      DOI: 10.4103/2153-3539.95129
      Issue No: Vol. 3, No. 1 (2012)
       
  • Investigation into diagnostic agreement using automated computer-assisted
           histopathology pattern recognition image analysis
    • Authors: Joshua D Webster, Aleksandra M Michalowski, Jennifer E Dwyer, Kara N Corps, Bih-Rong Wei, Tarja Juopperi, Shelley B Hoover, R Mark Simpson
      Pages: 18 - 18
      Abstract: Joshua D Webster, Aleksandra M Michalowski, Jennifer E Dwyer, Kara N Corps, Bih-Rong Wei, Tarja Juopperi, Shelley B Hoover, R Mark Simpson

      Journal of Pathology Informatics 2012 3(1):18-18

      The extent to which histopathology pattern recognition image analysis (PRIA) agrees with microscopic assessment has not been established. Thus, a commercial PRIA platform was evaluated in two applications using whole-slide images. Substantial agreement, lacking significant constant or proportional errors, between PRIA and manual morphometric image segmentation was obtained for pulmonary metastatic cancer areas (Passing/Bablok regression). Bland-Altman analysis indicated heteroscedastic measurements and tendency toward increasing variance with increasing tumor burden, but no significant trend in mean bias. The average between-methods percent tumor content difference was -0.64. Analysis of between-methods measurement differences relative to the percent tumor magnitude revealed that method disagreement had an impact primarily in the smallest measurements (tumor burden 0.988, indicating high reproducibility for both methods, yet PRIA reproducibility was superior (C.V.: PRIA = 7.4, manual = 17.1). Evaluation of PRIA on morphologically complex teratomas led to diagnostic agreement with pathologist assessments of pluripotency on subsets of teratomas. Accommodation of the diversity of teratoma histologic features frequently resulted in detrimental trade-offs, increasing PRIA error elsewhere in images. PRIA error was nonrandom and influenced by variations in histomorphology. File-size limitations encountered while training algorithms and consequences of spectral image processing dominance contributed to diagnostic inaccuracies experienced for some teratomas. PRIA appeared better suited for tissues with limited phenotypic diversity. Technical improvements may enhance diagnostic agreement, and consistent pathologist input will benefit further development and application of PRIA.
      Citation: Journal of Pathology Informatics 2012 3(1):18-18
      PubDate: Wed,18 Apr 2012
      DOI: 10.4103/2153-3539.95130
      Issue No: Vol. 3, No. 1 (2012)
       
  • Estrogen receptor testing and 10-year mortality from breast cancer: A
           model for determining testing strategy
    • Authors: Christopher Naugler
      Pages: 19 - 19
      Abstract: Christopher Naugler

      Journal of Pathology Informatics 2012 3(1):19-19

      Background: The use of adjuvant tamoxifen therapy in the treatment of estrogen receptor (ER) expressing breast carcinomas represents a major advance in personalized cancer treatment. Because there is no benefit (and indeed there is increased morbidity and mortality) associated with the use of tamoxifen therapy in ER-negative breast cancer, its use is restricted to women with ER expressing cancers. However, correctly classifying cancers as ER positive or negative has been challenging given the high reported false negative test rates for ER expression in surgical specimens. In this paper I model practice recommendations using published information from clinical trials to address the question of whether there is a false negative test rate above which it is more efficacious to forgo ER testing and instead treat all patients with tamoxifen regardless of ER test results. Methods: I used data from randomized clinical trials to model two different hypothetical treatment strategies: (1) the current strategy of treating only ER positive women with tamoxifen and (2) an alternative strategy where all women are treated with tamoxifen regardless of ER test results. The variables used in the model are literature-derived survival rates of the different combinations of ER positivity and treatment with tamoxifen, varying true ER positivity rates and varying false negative ER testing rates. The outcome variable was hypothetical 10-year survival. Results: The model predicted that there will be a range of true ER rates and false negative test rates above which it would be more efficacious to treat all women with breast cancer with tamoxifen and forgo ER testing. This situation occurred with high true positive ER rates and false negative ER test rates in the range of 20-30%. Conclusions: It is hoped that this model will provide an example of the potential importance of diagnostic error on clinical outcomes and furthermore will give an example of how the effect of that error could be modeled using real-world data from clinical trials.
      Citation: Journal of Pathology Informatics 2012 3(1):19-19
      PubDate: Sat,28 Apr 2012
      DOI: 10.4103/2153-3539.95452
      Issue No: Vol. 3, No. 1 (2012)
       
  • Computer-assisted imaging algorithms facilitate histomorphometric
           quantification of kidney damage in rodent renal failure models
    • Authors: Marcin Klapczynski, Gerard D Gagne, Sherry J Morgan, Kelly J Larson, Bruce E LeRoy, Eric A Blomme, Bryan F Cox, Eugene W Shek
      Pages: 20 - 20
      Abstract: Marcin Klapczynski, Gerard D Gagne, Sherry J Morgan, Kelly J Larson, Bruce E LeRoy, Eric A Blomme, Bryan F Cox, Eugene W Shek

      Journal of Pathology Informatics 2012 3(1):20-20

      Introduction: Surgical 5/6 nephrectomy and adenine-induced kidney failure in rats are frequently used models of progressive renal failure. In both models, rats develop significant morphological changes in the kidneys and quantification of these changes can be used to measure the efficacy of prophylactic or therapeutic approaches. In this study, the Aperio Genie Pattern Recognition technology, along with the Positive Pixel Count, Nuclear and Rare Event algorithms were used to quantify histological changes in both rat renal failure models. Methods: Analysis was performed on digitized slides of whole kidney sagittal sections stained with either hematoxylin and eosin or immunohistochemistry with an anti-nestin antibody to identify glomeruli, regenerating tubular epithelium, and tubulointerstitial myofibroblasts. An anti-polymorphonuclear neutrophil (PMN) antibody was also used to investigate neutrophil tissue infiltration. Results: Image analysis allowed for rapid and accurate quantification of relevant histopathologic changes such as increased cellularity and expansion of glomeruli, renal tubular dilatation, and degeneration, tissue inflammation, and mineral aggregation. The algorithms provided reliable and consistent results in both control and experimental groups and presented a quantifiable degree of damage associated with each model. Conclusion: These algorithms represent useful tools for the uniform and reproducible characterization of common histomorphologic features of renal injury in rats.
      Citation: Journal of Pathology Informatics 2012 3(1):20-20
      PubDate: Sat,28 Apr 2012
      DOI: 10.4103/2153-3539.95456
      Issue No: Vol. 3, No. 1 (2012)
       
  • Managing beyond the laboratory information system
    • Authors: Gregory J Buffone
      Pages: 21 - 21
      Abstract: Gregory J Buffone

      Journal of Pathology Informatics 2012 3(1):21-21


      Citation: Journal of Pathology Informatics 2012 3(1):21-21
      PubDate: Thu,24 May 2012
      DOI: 10.4103/2153-3539.96156
      Issue No: Vol. 3, No. 1 (2012)
       
  • Review of advanced imaging techniques
    • Authors: Yu Chen, Chia-Pin Liang, Yang Liu, Andrew H Fischer, Anil V Parwani, Liron Pantanowitz
      Pages: 22 - 22
      Abstract: Yu Chen, Chia-Pin Liang, Yang Liu, Andrew H Fischer, Anil V Parwani, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):22-22

      Pathology informatics encompasses digital imaging and related applications. Several specialized microscopy techniques have emerged which permit the acquisition of digital images ("optical biopsies") at high resolution. Coupled with fiber-optic and micro-optic components, some of these imaging techniques (e.g., optical coherence tomography) are now integrated with a wide range of imaging devices such as endoscopes, laparoscopes, catheters, and needles that enable imaging inside the body. These advanced imaging modalities have exciting diagnostic potential and introduce new opportunities in pathology. Therefore, it is important that pathology informaticists understand these advanced imaging techniques and the impact they have on pathology. This paper reviews several recently developed microscopic techniques, including diffraction-limited methods (e.g., confocal microscopy, 2-photon microscopy, 4Pi microscopy, and spatially modulated illumination microscopy) and subdiffraction techniques (e.g., photoactivated localization microscopy, stochastic optical reconstruction microscopy, and stimulated emission depletion microscopy). This article serves as a primer for pathology informaticists, highlighting the fundamentals and applications of advanced optical imaging techniques.
      Citation: Journal of Pathology Informatics 2012 3(1):22-22
      PubDate: Mon,28 May 2012
      Issue No: Vol. 3, No. 1 (2012)
       
  • The feasibility of using natural language processing to extract clinical
           information from breast pathology reports
    • Authors: Julliette M Buckley, Suzanne B Coopey, John Sharko, Fernanda Polubriaginof, Brian Drohan, Ahmet K Belli, Elizabeth M. H. Kim, Judy E Garber, Barbara L Smith, Michele A Gadd, Michelle C Specht, Constance A Roche, Thomas M Gudewicz, Kevin S Hughes
      Pages: 23 - 23
      Abstract: Julliette M Buckley, Suzanne B Coopey, John Sharko, Fernanda Polubriaginof, Brian Drohan, Ahmet K Belli, Elizabeth M. H. Kim, Judy E Garber, Barbara L Smith, Michele A Gadd, Michelle C Specht, Constance A Roche, Thomas M Gudewicz, Kevin S Hughes

      Journal of Pathology Informatics 2012 3(1):23-23

      Objective: The opportunity to integrate clinical decision support systems into clinical practice is limited due to the lack of structured, machine readable data in the current format of the electronic health record. Natural language processing has been designed to convert free text into machine readable data. The aim of the current study was to ascertain the feasibility of using natural language processing to extract clinical information from >76,000 breast pathology reports. Approach and Procedure: Breast pathology reports from three institutions were analyzed using natural language processing software (Clearforest, Waltham, MA) to extract information on a variety of pathologic diagnoses of interest. Data tables were created from the extracted information according to date of surgery, side of surgery, and medical record number. The variety of ways in which each diagnosis could be represented was recorded, as a means of demonstrating the complexity of machine interpretation of free text. Results: There was widespread variation in how pathologists reported common pathologic diagnoses. We report, for example, 124 ways of saying invasive ductal carcinoma and 95 ways of saying invasive lobular carcinoma. There were >4000 ways of saying invasive ductal carcinoma was not present. Natural language processor sensitivity and specificity were 99.1% and 96.5% when compared to expert human coders. Conclusion: We have demonstrated how a large body of free text medical information such as seen in breast pathology reports, can be converted to a machine readable format using natural language processing, and described the inherent complexities of the task.
      Citation: Journal of Pathology Informatics 2012 3(1):23-23
      PubDate: Sat,30 Jun 2012
      DOI: 10.4103/2153-3539.97788
      Issue No: Vol. 3, No. 1 (2012)
       
  • Image microarrays derived from tissue microarrays (IMA-TMA): New resource
           for computer-aided diagnostic algorithm development
    • Authors: Jennifer A Hipp, Jason D Hipp, Megan Lim, Gaurav Sharma, Lauren B Smith, Stephen M Hewitt, Ulysses G. J. Balis
      Pages: 24 - 24
      Abstract: Jennifer A Hipp, Jason D Hipp, Megan Lim, Gaurav Sharma, Lauren B Smith, Stephen M Hewitt, Ulysses G. J. Balis

      Journal of Pathology Informatics 2012 3(1):24-24

      Background: Conventional tissue microarrays (TMAs) consist of cores of tissue inserted into a recipient paraffin block such that a tissue section on a single glass slide can contain numerous patient samples in a spatially structured pattern. Scanning TMAs into digital slides for subsequent analysis by computer-aided diagnostic (CAD) algorithms all offers the possibility of evaluating candidate algorithms against a near-complete repertoire of variable disease morphologies. This parallel interrogation approach simplifies the evaluation, validation, and comparison of such candidate algorithms. A recently developed digital tool, digital core (dCORE), and image microarray maker (iMAM) enables the capture of uniformly sized and resolution-matched images, with these representing key morphologic features and fields of view, aggregated into a single monolithic digital image file in an array format, which we define as an image microarray (IMA). We further define the TMA-IMA construct as IMA-based images derived from whole slide images of TMAs themselves. Methods: Here we describe the first combined use of the previously described dCORE and iMAM tools, toward the goal of generating a higher-order image construct, with multiple TMA cores from multiple distinct conventional TMAs assembled as a single digital image montage. This image construct served as the basis of the carrying out of a massively parallel image analysis exercise, based on the use of the previously described spatially invariant vector quantization (SIVQ) algorithm. Results: Multicase, multifield TMA-IMAs of follicular lymphoma and follicular hyperplasia were separately rendered, using the aforementioned tools. Each of these two IMAs contained a distinct spectrum of morphologic heterogeneity with respect to both tingible body macrophage (TBM) appearance and apoptotic body morphology. SIVQ-based pattern matching, with ring vectors selected to screen for either tingible body macrophages or apoptotic bodies, was subsequently carried out on the differing TMA-IMAs, with attainment of excellent discriminant classification between the two diagnostic classes. Conclusion: The TMA-IMA construct enables and accelerates high-throughput multicase, multifield based image feature discovery and classification, thus simplifying the development, validation, and comparison of CAD algorithms in settings where the heterogeneity of diagnostic feature morphologic is a significant factor.
      Citation: Journal of Pathology Informatics 2012 3(1):24-24
      PubDate: Thu,12 Jul 2012
      DOI: 10.4103/2153-3539.98168
      Issue No: Vol. 3, No. 1 (2012)
       
  • ImageJS: Personalized, participated, pervasive, and reproducible image
           bioinformatics in the web browser
    • Authors: Jonas S Almeida, Egiebade E Iriabho, Vijaya L Gorrepati, Sean R Wilkinson, Alexander Grüneberg, David E Robbins, James R Hackney
      Pages: 25 - 25
      Abstract: Jonas S Almeida, Egiebade E Iriabho, Vijaya L Gorrepati, Sean R Wilkinson, Alexander Grüneberg, David E Robbins, James R Hackney

      Journal of Pathology Informatics 2012 3(1):25-25

      Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results : Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions : The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation."
      Citation: Journal of Pathology Informatics 2012 3(1):25-25
      PubDate: Fri,20 Jul 2012
      DOI: 10.4103/2153-3539.98813
      Issue No: Vol. 3, No. 1 (2012)
       
  • Utilization and utility of clinical laboratory reports with graphical
           elements
    • Authors: Brian H Shirts, Nichole Larsen, Brian R Jackson
      Pages: 26 - 26
      Abstract: Brian H Shirts, Nichole Larsen, Brian R Jackson

      Journal of Pathology Informatics 2012 3(1):26-26

      Background: Graphical reports that contain charts, images, and tables have potential to convey information more effectively than text-based reports; however, studies have not measured how much clinicians value such features. We sought to identify factors that might influence the utilization of reports with graphical elements postulating that this is a surrogate for relative clinical utility of these graphical elements. Materials and Methods: We implemented a pilot project at ARUP laboratories to develop online enhanced laboratory test reports that contained graphical elements. We monitored on-demand clinician access to reports generated for 48 reportable tests over 22 months. We evaluated utilization of reports with graphical elements by clinicians at all institutions that use ARUP as a reference laboratory using descriptive statistics, regression, and meta-analysis tools to evaluate groups of similar test reports. Results: Median download rate by test was 8.6% with high heterogeneity in download rates between tests. Test reports with additional graphical elements were not necessarily downloaded more often than reports without these elements. Recently implemented tests and tests reporting abnormal results were associated with higher download rates (P < 0.01). Higher volume tests were associated with lower download rates (P = 0.03). Conclusions: In select cases graphical information may be clinically useful, particularly for less frequently ordered tests and in on reports of abnormal results. The utilization data presented could be used as a reference point for other laboratories planning on implementing graphical reporting. However, between-test heterogeneity was high and in many cases graphical elements may add little clinical utility, particularly if these merely reinforce information already contained in text based reports.
      Citation: Journal of Pathology Informatics 2012 3(1):26-26
      PubDate: Sat,25 Aug 2012
      DOI: 10.4103/2153-3539.100145
      Issue No: Vol. 3, No. 1 (2012)
       
  • Diagnosis of dysplasia in upper gastro-intestinal tract biopsies through
           digital microscopy
    • Authors: Dorina Gui, Galen Cortina, Bita Naini, Steve Hart, Garrett Gerney, David Dawson, Sarah Dry
      Pages: 27 - 27
      Abstract: Dorina Gui, Galen Cortina, Bita Naini, Steve Hart, Garrett Gerney, David Dawson, Sarah Dry

      Journal of Pathology Informatics 2012 3(1):27-27

      Background: Whole slide digital imaging (WSDI) offers an alternative to glass slides for diagnostic interpretation. While prior work has concentrated on the use of whole slide digital imaging for routine diagnostic cases, this study focuses on diagnostic interpretation of digital images for a highly challenging area, upper gastro-intestinal (GI) dysplasia. The aim of this study is to study the accuracy and efficiency of WSDI in the diagnosis of upper GI tract dysplasia. Materials and Methods: Forty-two hematoxylin and eosin (H and E)-stained slides representing negative, indefinite, low grade and high grade dysplasia were selected and scanned at 20x (Aperio XT). Four attending GI pathologists reviewed the WSDI, then glass slides, with at least 3-4 weeks between each media; glass slides were re-reviewed 16-18 months later. Results: Intraobserver variability for three clinically relevant categories (negative, indefinite/low grade, high grade) was wider for WSDI to glass (kappa range 0.36-0.78) than glass to glass (kappa range 0.58-0.75). In comparison to glass slide review, WSDI review required more time and was associated with an unexpected trend toward downgrading dysplasia. Conclusions: Our results suggest: (1) upper GI dysplasia can be diagnosed using WSDI with similar intraobserver reproducibility as for glass slides; however, this is not true for all pathologists; (2) pathologists may have a tendency to downgrade dysplasia in digital images; and (3) pathologists who use WSDI for interpretation of GI dysplasia cases may benefit from regular, on-going, re-review of paired digital and glass images to ensure the most accurate utilization of digital technology, at least in the early stages of implementation.
      Citation: Journal of Pathology Informatics 2012 3(1):27-27
      PubDate: Sat,25 Aug 2012
      DOI: 10.4103/2153-3539.100149
      Issue No: Vol. 3, No. 1 (2012)
       
  • Dynamic nonrobotic telemicroscopy via skype: A cost effective solution to
           teleconsultation
    • Authors: Sahussapont J Sirintrapun, Adela Cimic
      Pages: 28 - 28
      Abstract: Sahussapont J Sirintrapun, Adela Cimic

      Journal of Pathology Informatics 2012 3(1):28-28

      Context: Skype is a peer to peer software application that has been historically used for voice and video calls, instant messaging, and file transfer over the Internet. Few studies are available using Skype specifically for telepathology. Aims: Our aim is to show that dynamic nonrobotic teleconsultation is possible and even effective via means of a standard microscope camera capable of live acquisition, Skype, an established broad band internet connection, and experienced pathologists. Settings and Design: Both the consulting "sending" pathologist and consultant "receiving" pathologist are reasonably experienced general surgical pathologists at junior attending level with several years of experience in sign out. Forty-five cases were chosen encompassing a broad range of surgical pathology specimens. The cases were prospectively evaluated with the consultant diagnosis used as a preliminary pathologic impression with the final diagnosis being confirmation. Materials and Methods: Versions of Skype 5.0 and above were used along with established broadband internet connections, usually between academic medical institutions. Results: Forty of forty-five cases (89%) were essentially concordant. In four of forty-five cases (9%), the consulting impression gave a differential, but favored an entity which did not match the final diagnosis. Only one case (2%) did the consulting impression not match the final diagnosis; a discordant opinion. Conclusions: The image quality via Skype screen sharing option is excellent. Essentially no lag time was seen. We have shown in our small pilot study that Skype is an effective cost-efficient means for teleconsultation, particularly in the setting of entity-related differential diagnoses in surgical pathology and when both the consulting and consultant pathologists are reasonably experienced.
      Citation: Journal of Pathology Informatics 2012 3(1):28-28
      PubDate: Sat,25 Aug 2012
      DOI: 10.4103/2153-3539.100150
      Issue No: Vol. 3, No. 1 (2012)
       
  • Experience with CellaVision DM96 for peripheral blood differentials in a
           large multi-center academic hospital system
    • Authors: Marian A Rollins-Raval, Jay S Raval, Lydia Contis
      Pages: 29 - 29
      Abstract: Marian A Rollins-Raval, Jay S Raval, Lydia Contis

      Journal of Pathology Informatics 2012 3(1):29-29

      Context and Aims: Rapid, accurate peripheral blood differentials are essential to maintain standards of patient care. CellaVision DM96 (CellaVision AB, Lund, Sweden) (CV) is an automated digital morphology and informatics system used to locate, pre-classify, store and transmit images of platelets, red and white blood cells to a trained technologist who confirms or edits CV cell classification. We assessed our experience with CV by evaluating sensitivity, specificity, positive predictive value and negative predictive value for CV in three different patient populations. Materials and Methods: We analyzed classification accuracy of CV for white blood cells, erythroblasts, platelets and artefacts over six months for three different university hospitals using CV. Results: CV classified 211,218 events for the adult cancer center; 51,699 events for the adult general hospital; and 8,009 events for the children's hospital with accuracy of CV being 93%, 87.3% and 95.4% respectively. Sensitivity and positive predictive value were
      Citation: Journal of Pathology Informatics 2012 3(1):29-29
      PubDate: Sat,25 Aug 2012
      DOI: 10.4103/2153-3539.100154
      Issue No: Vol. 3, No. 1 (2012)
       
  • Different tracks for pathology informatics fellowship training:
           Experiences of and input from trainees in a large multisite fellowship
           program
    • Authors: Bruce P Levy, David S McClintock, Roy E Lee, William J Lane, Veronica E Klepeis, Jason M Baron, Maristela L Onozato, JiYeon Kim, Victor Brodsky, Bruce Beckwith, Frank Kuo, John R Gilbertson
      Pages: 30 - 30
      Abstract: Bruce P Levy, David S McClintock, Roy E Lee, William J Lane, Veronica E Klepeis, Jason M Baron, Maristela L Onozato, JiYeon Kim, Victor Brodsky, Bruce Beckwith, Frank Kuo, John R Gilbertson

      Journal of Pathology Informatics 2012 3(1):30-30

      Background: Pathology Informatics is a new field; a field that is still defining itself even as it begins the formalization, accreditation, and board certification process. At the same time, Pathology itself is changing in a variety of ways that impact informatics, including subspecialization and an increased use of data analysis. In this paper, we examine how these changes impact both the structure of Pathology Informatics fellowship programs and the fellows' goals within those programs. Materials and Methods: As part of our regular program review process, the fellows evaluated the value and effectiveness of our existing fellowship tracks (Research Informatics, Clinical Two-year Focused Informatics, Clinical One-year Focused Informatics, and Clinical 1 + 1 Subspecialty Pathology and Informatics). They compared their education, informatics background, and anticipated career paths and analyzed them for correlations between those parameters and the fellowship track chosen. All current and past fellows of the program were actively involved with the project. Results: Fellows' anticipated career paths correlated very well with the specific tracks in the program. A small set of fellows (Clinical - one or two year - Focused Informatics tracks) anticipated clinical careers primarily focused in informatics (Director of Informatics). The majority of the fellows, however, anticipated a career practicing in a Pathology subspecialty, using their informatics training to enhance that practice (Clinical 1 + 1 Subspecialty Pathology and Informatics Track). Significantly, all fellows on this track reported they would not have considered a Clinical Two-year Focused Informatics track if it was the only track offered. The Research and the Clinical One-year Focused Informatics tracks each displayed unique value for different situations. Conclusions: It seems a "one size fits all" fellowship structure does not fit the needs of the majority of potential Pathology Informatics candidates. Increasingly, these fellowships must be able to accommodate the needs of candidates anticipating a wide range of Pathology Informatics career paths, be able to accommodate Pathology's increasingly subspecialized structure, and do this in a way that respects the multiple fellowships needed to become a subspecialty pathologist and informatician. This is further complicated as Pathology Informatics begins to look outward and takes its place in the growing, and still ill-defined, field of Clinical Informatics, a field that is not confined to just one medical specialty, to one way of practicing medicine, or to one way of providing patient care.
      Citation: Journal of Pathology Informatics 2012 3(1):30-30
      PubDate: Thu,30 Aug 2012
      DOI: 10.4103/2153-3539.100362
      Issue No: Vol. 3, No. 1 (2012)
       
  • A core curriculum for clinical fellowship training in pathology
           informatics
    • Authors: David S McClintock, Bruce P Levy, William J Lane, Roy E Lee, Jason M Baron, Veronica E Klepeis, Maristela L Onozato, JiYeon Kim, Anand S Dighe, Bruce A Beckwith, Frank Kuo, Stephen Black-Schaffer, John R Gilbertson
      Pages: 31 - 31
      Abstract: David S McClintock, Bruce P Levy, William J Lane, Roy E Lee, Jason M Baron, Veronica E Klepeis, Maristela L Onozato, JiYeon Kim, Anand S Dighe, Bruce A Beckwith, Frank Kuo, Stephen Black-Schaffer, John R Gilbertson

      Journal of Pathology Informatics 2012 3(1):31-31

      Background: In 2007, our healthcare system established a clinical fellowship program in Pathology Informatics. In 2010 a core didactic course was implemented to supplement the fellowship research and operational rotations. In 2011, the course was enhanced by a formal, structured core curriculum and reading list. We present and discuss our rationale and development process for the Core Curriculum and the role it plays in our Pathology Informatics Fellowship Training Program. Materials and Methods: The Core Curriculum for Pathology Informatics was developed, and is maintained, through the combined efforts of our Pathology Informatics Fellows and Faculty. The curriculum was created with a three-tiered structure, consisting of divisions, topics, and subtopics. Primary (required) and suggested readings were selected for each subtopic in the curriculum and incorporated into a curated reading list, which is reviewed and maintained on a regular basis. Results: Our Core Curriculum is composed of four major divisions, 22 topics, and 92 subtopics that cover the wide breadth of Pathology Informatics. The four major divisions include: (1) Information Fundamentals, (2) Information Systems, (3) Workflow and Process, and (4) Governance and Management. A detailed, comprehensive reading list for the curriculum is presented in the Appendix to the manuscript and contains 570 total readings (current as of March 2012). Discussion: The adoption of a formal, core curriculum in a Pathology Informatics fellowship has significant impacts on both fellowship training and the general field of Pathology Informatics itself. For a fellowship, a core curriculum defines a basic, common scope of knowledge that the fellowship expects all of its graduates will know, while at the same time enhancing and broadening the traditional fellowship experience of research and operational rotations. For the field of Pathology Informatics itself, a core curriculum defines to the outside world, including departments, companies, and health systems considering hiring a pathology informatician, the core knowledge set expected of a person trained in the field and, more fundamentally, it helps to define the scope of the field within Pathology and healthcare in general.
      Citation: Journal of Pathology Informatics 2012 3(1):31-31
      PubDate: Thu,30 Aug 2012
      DOI: 10.4103/2153-3539.100364
      Issue No: Vol. 3, No. 1 (2012)
       
  • Use of a wiki as an interactive teaching tool in pathology residency
           education: Experience with a genomics, research, and informatics in
           pathology course
    • Authors: Seung Park, Anil Parwani, Trevor MacPherson, Liron Pantanowitz
      Pages: 32 - 32
      Abstract: Seung Park, Anil Parwani, Trevor MacPherson, Liron Pantanowitz

      Journal of Pathology Informatics 2012 3(1):32-32

      Background: The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in "Web 2.0") in a combined informatics and genomics course could both (1) serve as an interactive, collaborative educational resource and reference and (2) actively engage trainees by requiring the creation and sharing of educational materials. Materials and Methods: A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP) was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software). Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki) and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics) given at our institution that did not utilize wikis. Results: Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12%) in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006). Conclusions: Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation is an effective mechanism for mastery of content. Future residents taking this course will continue to build on this wiki, keeping content current, and thereby benefit from this collaborative teaching tool.
      Citation: Journal of Pathology Informatics 2012 3(1):32-32
      PubDate: Thu,30 Aug 2012
      DOI: 10.4103/2153-3539.100366
      Issue No: Vol. 3, No. 1 (2012)
       
  • The analysis of image feature robustness using cometcloud
    • Authors: Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J Foran, Lin Yang
      Pages: 33 - 33
      Abstract: Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J Foran, Lin Yang

      Journal of Pathology Informatics 2012 3(1):33-33

      The robustness of image features is a very important consideration in quantitative image analysis. The objective of this paper is to investigate the robustness of a range of image texture features using hematoxylin stained breast tissue microarray slides which are assessed while simulating different imaging challenges including out of focus, changes in magnification and variations in illumination, noise, compression, distortion, and rotation. We employed five texture analysis methods and tested them while introducing all of the challenges listed above. The texture features that were evaluated include co-occurrence matrix, center-symmetric auto-correlation, texture feature coding method, local binary pattern, and texton. Due to the independence of each transformation and texture descriptor, a network structured combination was proposed and deployed on the Rutgers private cloud. The experiments utilized 20 randomly selected tissue microarray cores. All the combinations of the image transformations and deformations are calculated, and the whole feature extraction procedure was completed in 70 minutes using a cloud equipped with 20 nodes. Center-symmetric auto-correlation outperforms all the other four texture descriptors but also requires the longest computational time. It is roughly 10 times slower than local binary pattern and texton. From a speed perspective, both the local binary pattern and texton features provided excellent performance for classification and content-based image retrieval.
      Citation: Journal of Pathology Informatics 2012 3(1):33-33
      PubDate: Fri,28 Sep 2012
      DOI: 10.4103/2153-3539.101782
      Issue No: Vol. 3, No. 1 (2012)
       
  • Interactive case vignettes utilizing simulated pathologist-clinician
           encounters with whole slide imaging and video tutorials of whole slide
           scans improves student understanding of disease processes
    • Authors: Adam J Horn, Donna Czarnecki, Subodh M Lele
      Pages: 34 - 34
      Abstract: Adam J Horn, Donna Czarnecki, Subodh M Lele

      Journal of Pathology Informatics 2012 3(1):34-34

      Background: One of the drawbacks of studying pathology in the second year of medical school in a classroom setting is the relatively limited exposure to patient encounters/clinical rotations, making it difficult to understand and fully appreciate the significance of the course material, specifically the molecular and tissue aspects of disease. In this study, we determined if case vignettes incorporating pathologist-clinician encounters with whole slide imaging (WSI) and narrated/annotated videos of whole slide (WS) scans in addition to clinical data improved student understanding of pathologic disease processes. Materials and Methods: Case vignettes were created for several genitourinary disease processes that utilized clinical data including narratives of pathologist-clinician encounters, WSI, and annotated video tutorials of WS scans (designed to simulate "double-heading"). The students were encouraged to view the virtual slide first, with the video tutorials being provided to offer additional assistance. The case vignettes were created to be interactive with a detailed explanation of each correct and incorrect question choice. The cases were made available to all second year medical students via a website and could be viewed only after completing a 10 question pre-test. A post-test could be completed after viewing all cases followed by a brief satisfaction survey. Results: Ninety-six students completed the pre-test with an average score of 7.7/10. Fifty-seven students completed the post-test with an average score of 9.4/10. Thirty-six students completed the satisfaction survey. 94% agreed or strongly agreed that this was a useful exercise and 91% felt that it helped them better understand the topics. Conclusion: The development of interactive case vignettes incorporating simulated pathologist-clinician encounters with WSI and video tutorials of WS scans helps to improve student enthusiasm to learn and grasp pathologic aspects of disease processes that lead to clinical therapeutic decision making.
      Citation: Journal of Pathology Informatics 2012 3(1):34-34
      PubDate: Fri,28 Sep 2012
      DOI: 10.4103/2153-3539.101786
      Issue No: Vol. 3, No. 1 (2012)
       
  • Use of contextual inquiry to understand anatomic pathology workflow:
           Implications for digital pathology adoption
    • Authors: Jonhan Ho, Orly Aridor, Anil V Parwani
      Pages: 35 - 35
      Abstract: Jonhan Ho, Orly Aridor, Anil V Parwani

      Journal of Pathology Informatics 2012 3(1):35-35

      Background: For decades anatomic pathology (AP) workflow have been a highly manual process based on the use of an optical microscope and glass slides. Recent innovations in scanning and digitizing of entire glass slides are accelerating a move toward widespread adoption and implementation of a workflow based on digital slides and their supporting information management software. To support the design of digital pathology systems and ensure their adoption into pathology practice, the needs of the main users within the AP workflow, the pathologists, should be identified. Contextual inquiry is a qualitative, user-centered, social method designed to identify and understand users' needs and is utilized for collecting, interpreting, and aggregating in-detail aspects of work. Objective: Contextual inquiry was utilized to document current AP workflow, identify processes that may benefit from the introduction of digital pathology systems, and establish design requirements for digital pathology systems that will meet pathologists' needs. Materials and Methods: Pathologists were observed and interviewed at a large academic medical center according to contextual inquiry guidelines established by Holtzblatt et al. 1998. Notes representing user-provided data were documented during observation sessions. An affinity diagram, a hierarchal organization of the notes based on common themes in the data, was created. Five graphical models were developed to help visualize the data including sequence, flow, artifact, physical, and cultural models. Results: A total of six pathologists were observed by a team of two researchers. A total of 254 affinity notes were documented and organized using a system based on topical hierarchy, including 75 third-level, 24 second-level, and five main-level categories, including technology, communication, synthesis/preparation, organization, and workflow. Current AP workflow was labor intensive and lacked scalability. A large number of processes that may possibly improve following the introduction of digital pathology systems were identified. These work processes included case management, case examination and review, and final case reporting. Furthermore, a digital slide system should integrate with the anatomic pathologic laboratory information system. Conclusions: To our knowledge, this is the first study that utilized the contextual inquiry method to document AP workflow. Findings were used to establish key requirements for the design of digital pathology systems.
      Citation: Journal of Pathology Informatics 2012 3(1):35-35
      PubDate: Fri,28 Sep 2012
      DOI: 10.4103/2153-3539.101794
      Issue No: Vol. 3, No. 1 (2012)
       
  • Feasibility of telecytopathology for rapid preliminary diagnosis of
           ultrasound-guided fine needle aspiration of axillary lymph nodes in a
           remote breast care center
    • Authors: Kamal K Khurana, Andra Kovalovsky, Deepa Masrani
      Pages: 36 - 36
      Abstract: Kamal K Khurana, Andra Kovalovsky, Deepa Masrani

      Journal of Pathology Informatics 2012 3(1):36-36

      Background: In the recent years, the advances in digital methods in pathology have resulted in the use of telecytology in the immediate assessment of fine needle aspiration (FNA) specimens. However, there is a need for organ-based and body site-specific studies on the use of telecytology for the immediate assessment of FNA to evaluate its pitfalls and limitations. We present our experience with the use of telecytology for on-site evaluation of ultrasound-guided FNA (USG-FNA) of axillary lymph nodes in a remote breast care center. Materials and Methods: Real-time images of Diff-Quik-stained cytology smears were obtained with an Olympus digital camera attached to an Olympus CX41 microscope and transmitted via ethernet by a cytotechnologist to a pathologist who rendered preliminary diagnosis while communicating with the on-site cytotechnologist over the Vocera system. The accuracy of the preliminary diagnosis was compared with the final diagnosis, retrospectively. Results: A total of 39 female patients (mean age: 50.5 years) seen at the breast care center underwent USG-FNA of 44 axillary nodes. Preliminary diagnoses of benign, suspicious/malignant, and unsatisfactory were 41, 52, and 7%, respectively. Only one of the 23 cases that were initially interpreted as benign was reclassified as suspicious on final cytologic diagnosis. Seventeen of 18 suspicious/malignant cases on initial cytology corresponded with a malignant diagnosis on final cytology. One suspicious case was reclassified as benign on final cytologic diagnosis. All unsatisfactory cases remained inadequate for final cytologic interpretation. The presence of additional material in the cell block and interpretative error were the main reasons for discrepancy, accounting for the two discrepant cases. Conclusions: This retrospective study demonstrates that the on-site telecytology evaluation of USG-FNA of axillary lymph nodes in patients at a remote breast care center was highly accurate compared with the final cytologic evaluation. It allows pathologists to use their time more efficiently and makes on-site evaluation at a remote site possible.
      Citation: Journal of Pathology Informatics 2012 3(1):36-36
      PubDate: Fri,28 Sep 2012
      DOI: 10.4103/2153-3539.101803
      Issue No: Vol. 3, No. 1 (2012)
       
  • Abstracts: Pathology Informatics 2012
    • Pages: 37 - 37
      Abstract:

      Journal of Pathology Informatics 2012 3(1):37-37


      Citation: Journal of Pathology Informatics 2012 3(1):37-37
      PubDate: Tue,9 Oct 2012
      Issue No: Vol. 3, No. 1 (2012)
       
  • Review of "Pathology informatics: Theory and practice" by L
           Pantanowitz, JM Tuthill, and UGJ Balis (Editors)
    • Authors: Myra L Wilkerson
      Pages: 38 - 38
      Abstract: Myra L Wilkerson

      Journal of Pathology Informatics 2012 3(1):38-38


      Citation: Journal of Pathology Informatics 2012 3(1):38-38
      PubDate: Wed,31 Oct 2012
      Issue No: Vol. 3, No. 1 (2012)
       
  • Evaluation of whole slide imaging for routine surgical pathology: Looking
           through a broader scope
    • Authors: Walter H Henricks
      Pages: 39 - 39
      Abstract: Walter H Henricks

      Journal of Pathology Informatics 2012 3(1):39-39


      Citation: Journal of Pathology Informatics 2012 3(1):39-39
      PubDate: Wed,31 Oct 2012
      DOI: 10.4103/2153-3539.103009
      Issue No: Vol. 3, No. 1 (2012)
       
  • Next generation sequencing in clinical medicine: Challenges and lessons
           for pathology and biomedical informatics
    • Authors: Rama R Gullapalli, Ketaki V Desai, Lucas Santana-Santos, Jeffrey A Kant, Michael J Becich
      Pages: 40 - 40
      Abstract: Rama R Gullapalli, Ketaki V Desai, Lucas Santana-Santos, Jeffrey A Kant, Michael J Becich

      Journal of Pathology Informatics 2012 3(1):40-40

      The Human Genome Project (HGP) provided the initial draft of mankind's DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS) techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage. Implementation of routine NGS data in cancer genomics is discussed along with potential pitfalls in the interpretation of the NGS data. The overarching importance of bioinformatics in the clinical implementation of NGS is emphasized. [7] We also review the issue of physician education which also is an important consideration for the successful implementation of NGS in the clinical workplace. NGS technologies represent a golden opportunity for the next generation of pathologists to be at the leading edge of the personalized medicine approaches coming our way. Often under-emphasized issues of data access and control as well as potential ethical implications of whole genome NGS sequencing are also discussed. Despite some challenges, it's hard not to be optimistic about the future of personalized genome sequencing and its potential impact on patient care and the advancement of knowledge of human biology and disease in the near future.
      Citation: Journal of Pathology Informatics 2012 3(1):40-40
      PubDate: Wed,31 Oct 2012
      DOI: 10.4103/2153-3539.103013
      Issue No: Vol. 3, No. 1 (2012)
       
  • Pathology informatics fellowship retreats: The use of interactive
           scenarios and case studies as pathology informatics teaching tools
    • Authors: Roy E Lee, David S McClintock, Ulysses J Balis, Jason M Baron, Michael J Becich, Bruce A Beckwith, Victor B Brodsky, Alexis B Carter, Anand S Dighe, Mehrvash Haghighi, Jason D Hipp, Walter H Henricks, Jiyeon Y Kim, Veronica E Klepseis, Frank C Kuo, William J Lane, Bruce P Levy, Maristela L Onozato, Seung L Park, John H Sinard, Mark J Tuthill, John R Gilbertson
      Pages: 41 - 41
      Abstract: Roy E Lee, David S McClintock, Ulysses J Balis, Jason M Baron, Michael J Becich, Bruce A Beckwith, Victor B Brodsky, Alexis B Carter, Anand S Dighe, Mehrvash Haghighi, Jason D Hipp, Walter H Henricks, Jiyeon Y Kim, Veronica E Klepseis, Frank C Kuo, William J Lane, Bruce P Levy, Maristela L Onozato, Seung L Park, John H Sinard, Mark J Tuthill, John R Gilbertson

      Journal of Pathology Informatics 2012 3(1):41-41

      Background: Last year, our pathology informatics fellowship added informatics-based interactive case studies to its existing educational platform of operational and research rotations, clinical conferences, a common core curriculum with an accompanying didactic course, and national meetings. Methods: The structure of the informatics case studies was based on the traditional business school case study format. Three different formats were used, varying in length from short, 15-minute scenarios to more formal multiple hour-long case studies. Case studies were presented over the course of three retreats (Fall 2011, Winter 2012, and Spring 2012) and involved both local and visiting faculty and fellows. Results: Both faculty and fellows found the case studies and the retreats educational, valuable, and enjoyable. From this positive feedback, we plan to incorporate the retreats in future academic years as an educational component of our fellowship program. Conclusions: Interactive case studies appear to be valuable in teaching several aspects of pathology informatics that are difficult to teach in more traditional venues (rotations and didactic class sessions). Case studies have become an important component of our fellowship's educational platform.
      Citation: Journal of Pathology Informatics 2012 3(1):41-41
      PubDate: Wed,28 Nov 2012
      DOI: 10.4103/2153-3539.103995
      Issue No: Vol. 3, No. 1 (2012)
       
  • Tissue microarray design and construction for scientific, industrial and
           diagnostic use
    • Authors: Daniela Pilla, Francesca M Bosisio, Roberto Marotta, Stefano Faggi, Paolo Forlani, Maurizio Falavigna, Ida Biunno, Emanuele Martella, Pasquale De Blasio, Simone Borghesi, Giorgio Cattoretti
      Pages: 42 - 42
      Abstract: Daniela Pilla, Francesca M Bosisio, Roberto Marotta, Stefano Faggi, Paolo Forlani, Maurizio Falavigna, Ida Biunno, Emanuele Martella, Pasquale De Blasio, Simone Borghesi, Giorgio Cattoretti

      Journal of Pathology Informatics 2012 3(1):42-42

      Context: In 2013 the high throughput technology known as Tissue Micro Array (TMA) will be fifteen years old. Its elements (design, construction and analysis) are intuitive and the core histopathology technique is unsophisticated, which may be a reason why has eluded a rigorous scientific scrutiny. The source of errors, particularly in specimen identification and how to control for it is unreported. Formal validation of the accuracy of segmenting (also known as de-arraying) hundreds of samples, pairing with the sample data is lacking. Aims: We wanted to address these issues in order to bring the technique to recognized standards of quality in TMA use for research, diagnostics and industrial purposes. Results: We systematically addressed the sources of error and used barcode-driven data input throughout the whole process including matching the design with a TMA virtual image and segmenting that image back to individual cases, together with the associated data. In addition we demonstrate on mathematical grounds that a TMA design, when superimposed onto the corresponding whole slide image, validates on each and every sample the correspondence between the image and patient's data. Conclusions: High throughput use of the TMA technology is a safe and efficient method for research, diagnosis and industrial use if all sources of errors are identified and addressed.
      Citation: Journal of Pathology Informatics 2012 3(1):42-42
      PubDate: Thu,20 Dec 2012
      DOI: 10.4103/2153-3539.104904
      Issue No: Vol. 3, No. 1 (2012)
       
  • Mouse cursor movement and eye tracking data as an indicator of
           pathologists' attention when viewing digital whole slide images
    • Authors: Vignesh Raghunath, Melissa O Braxton, Stephanie A Gagnon, Tad T Brunyé, Kimberly H Allison, Lisa M Reisch, Donald L Weaver, Joann G Elmore, Linda G Shapiro
      Pages: 43 - 43
      Abstract: Vignesh Raghunath, Melissa O Braxton, Stephanie A Gagnon, Tad T Brunyé, Kimberly H Allison, Lisa M Reisch, Donald L Weaver, Joann G Elmore, Linda G Shapiro

      Journal of Pathology Informatics 2012 3(1):43-43

      Context: Digital pathology has the potential to dramatically alter the way pathologists work, yet little is known about pathologists' viewing behavior while interpreting digital whole slide images. While tracking pathologist eye movements when viewing digital slides may be the most direct method of capturing pathologists' viewing strategies, this technique is cumbersome and technically challenging to use in remote settings. Tracking pathologist mouse cursor movements may serve as a practical method of studying digital slide interpretation, and mouse cursor data may illuminate pathologists' viewing strategies and time expenditures in their interpretive workflow. Aims: To evaluate the utility of mouse cursor movement data, in addition to eye-tracking data, in studying pathologists' attention and viewing behavior. Settings and Design: Pathologists (N = 7) viewed 10 digital whole slide images of breast tissue that were selected using a random stratified sampling technique to include a range of breast pathology diagnoses (benign/atypia, carcinoma in situ, and invasive breast cancer). A panel of three expert breast pathologists established a consensus diagnosis for each case using a modified Delphi approach. Materials and Methods: Participants' foveal vision was tracked using SensoMotoric Instruments RED 60 Hz eye-tracking system. Mouse cursor movement was tracked using a custom MATLAB script. Statistical Analysis Used: Data on eye-gaze and mouse cursor position were gathered at fixed intervals and analyzed using distance comparisons and regression analyses by slide diagnosis and pathologist expertise. Pathologists' accuracy (defined as percent agreement with the expert consensus diagnoses) and efficiency (accuracy and speed) were also analyzed. Results: Mean viewing time per slide was 75.2 seconds (SD = 38.42). Accuracy (percent agreement with expert consensus) by diagnosis type was: 83% (benign/atypia); 48% (carcinoma in situ); and 93% (invasive). Spatial coupling was close between eye-gaze and mouse cursor positions (highest frequency &#8710;x was 4.00px (SD = 16.10), and &#8710;y was 37.50px (SD = 28.08)). Mouse cursor position moderately predicted eye gaze patterns (Rx = 0.33 and Ry = 0.21). Conclusions: Data detailing mouse cursor movements may be a useful addition to future studies of pathologists' accuracy and efficiency when using digital pathology.
      Citation: Journal of Pathology Informatics 2012 3(1):43-43
      PubDate: Thu,20 Dec 2012
      DOI: 10.4103/2153-3539.104905
      Issue No: Vol. 3, No. 1 (2012)
       
  • Custom software development for use in a clinical laboratory
    • Authors: John H Sinard, Peter Gershkovich
      Pages: 44 - 44
      Abstract: John H Sinard, Peter Gershkovich

      Journal of Pathology Informatics 2012 3(1):44-44

      In-house software development for use in a clinical laboratory is a controversial issue. Many of the objections raised are based on outdated software development practices, an exaggeration of the risks involved, and an underestimation of the benefits that can be realized. Buy versus build analyses typically do not consider total costs of ownership, and unfortunately decisions are often made by people who are not directly affected by the workflow obstacles or benefits that result from those decisions. We have been developing custom software for clinical use for over a decade, and this article presents our perspective on this practice. A complete analysis of the decision to develop or purchase must ultimately examine how the end result will mesh with the departmental workflow, and custom-developed solutions typically can have the greater positive impact on efficiency and productivity, substantially altering the decision balance sheet. Involving the end-users in preparation of the functional specifications is crucial to the success of the process. A large development team is not needed, and even a single programmer can develop significant solutions. Many of the risks associated with custom development can be mitigated by a well-structured development process, use of open-source tools, and embracing an agile development philosophy. In-house solutions have the significant advantage of being adaptable to changing departmental needs, contributing to efficient and higher quality patient care.
      Citation: Journal of Pathology Informatics 2012 3(1):44-44
      PubDate: Thu,20 Dec 2012
      DOI: 10.4103/2153-3539.104906
      Issue No: Vol. 3, No. 1 (2012)
       
  • Experience with multimodality telepathology at the University of
           Pittsburgh Medical Center
    • Authors: Liron Pantanowitz, Clayton A Wiley, Anthony Demetris, Andrew Lesniak, Ishtiaque Ahmed, William Cable, Lydia Contis, Anil V Parwani
      Pages: 45 - 45
      Abstract: Liron Pantanowitz, Clayton A Wiley, Anthony Demetris, Andrew Lesniak, Ishtiaque Ahmed, William Cable, Lydia Contis, Anil V Parwani

      Journal of Pathology Informatics 2012 3(1):45-45

      Several modes of telepathology exist including static (store-and-forward), dynamic (live video streaming or robotic microscopy), and hybrid technology involving whole slide imaging (WSI). Telepathology has been employed at the University of Pittsburgh Medical Center (UPMC) for over a decade at local, national, and international sites. All modes of telepathology have been successfully utilized to exploit our institutions subspecialty expertise and to compete for pathology services. This article discusses the experience garnered at UPMC with each of these teleconsultation methods. Static and WSI telepathology systems have been utilized for many years in transplant pathology using a private network and client-server architecture. Only minor clinically significant differences of opinion were documented. In hematopathology, the CellaVision&#174; system is used to transmit, via email, static images of blood cells in peripheral blood smears for remote interpretation. While live video streaming has remained the mode of choice for providing immediate adequacy assessment of cytology specimens by telecytology, other methods such as robotic microscopy have been validated and shown to be effective. Robotic telepathology has been extensively used to remotely interpret intra-operative neuropathology consultations (frozen sections). Adoption of newer technology and increased pathologist experience has improved accuracy and deferral rates in teleneuropathology. A digital pathology consultation portal (https://pathconsult.upmc.com/) was recently created at our institution to facilitate digital pathology second opinion consults, especially for WSI. The success of this web-based tool is the ability to handle vendor agnostic, large image files of digitized slides, and ongoing user-friendly customization for clients and teleconsultants. It is evident that the practice of telepathology at our institution has evolved in concert with advances in technology and user experience. Early and continued adoption of telepathology has promoted additional digital pathology resources that are now being leveraged for other clinical, educational, and research purposes.
      Citation: Journal of Pathology Informatics 2012 3(1):45-45
      PubDate: Thu,20 Dec 2012
      DOI: 10.4103/2153-3539.104907
      Issue No: Vol. 3, No. 1 (2012)
       
  • Whole slide imaging for educational purposes
    • Authors: Liron Pantanowitz, Janusz Szymas, Yukako Yagi, David Wilbur
      Pages: 46 - 46
      Abstract: Liron Pantanowitz, Janusz Szymas, Yukako Yagi, David Wilbur

      Journal of Pathology Informatics 2012 3(1):46-46

      Digitized slides produced by whole slide image scanners can be easily shared over a network or by transferring image files to optical or other data storage devices. Navigation of digitized slides is interactive and intended to simulate viewing glass slides with a microscope (virtual microscopy). Image viewing software permits users to edit, annotate, analyze, and easily share whole slide images (WSI). As a result, WSI have begun to replace the traditional light microscope, offering a myriad of opportunities for education. This article focuses on current applications of WSI in education and proficiency testing. WSI has been successfully explored for graduate education (medical, dental, and veterinary schools), training of pathology residents, as an educational tool in allied pathology schools (e.g., cytotechnology), for virtual tracking and tutoring, tele-education (tele-conferencing), e-learning, virtual workshops, at tumor boards, with interactive publications, and on examinations. WSI supports flexible and cost-effective distant learning and augments problem-oriented teaching, competency evaluation, and proficiency testing. WSI viewed on touchscreen displays and with tablet technology are especially beneficial for education. Further investigation is necessary to develop superior WSI applications that better support education and to design viewing stations with ergonomic tools that improve the WSI-human interface and navigation of virtual slides. Studies to determine the impact of training pathologists without exposure to actual glass slides are also needed.
      Citation: Journal of Pathology Informatics 2012 3(1):46-46
      PubDate: Thu,20 Dec 2012
      DOI: 10.4103/2153-3539.104908
      Issue No: Vol. 3, No. 1 (2012)
       
  • A tribute to Jeffrey A. Kant, MD, PhD
    • Authors: Alexis B Carter, Ramachandra R Gullapalli, Jill M Hagenkord, Hyunseok P Kang, Federico A Monzon, Thomas M Williams
      Pages: 47 - 47
      Abstract: Alexis B Carter, Ramachandra R Gullapalli, Jill M Hagenkord, Hyunseok P Kang, Federico A Monzon, Thomas M Williams

      Journal of Pathology Informatics 2012 3(1):47-47


      Citation: Journal of Pathology Informatics 2012 3(1):47-47
      PubDate: Mon,31 Dec 2012
      DOI: 10.4103/2153-3539.105273
      Issue No: Vol. 3, No. 1 (2012)
       
  • Multi-field-of-view strategy for image-based outcome prediction of
           multi-parametric estrogen receptor-positive breast cancer histopathology:
           Comparison to Oncotype DX
    • Authors: Ajay Basavanhally, Michael Feldman, Natalie Shih, Carolyn Mies, John Tomaszewski, Shridar Ganesan, Anant Madabhushi
      Pages: 1 - 1
      Abstract: Ajay Basavanhally, Michael Feldman, Natalie Shih, Carolyn Mies, John Tomaszewski, Shridar Ganesan, Anant Madabhushi

      Journal of Pathology Informatics 2011 2(2):1-1

      In this paper, we attempt to quantify the prognostic information embedded in multi-parametric histologic biopsy images to predict disease aggressiveness in estrogen receptor-positive (ER+) breast cancers (BCa). The novel methodological contribution is in the use of a multi-field-of-view (multi-FOV) framework for integrating image-based information from differently stained histopathology slides. The multi-FOV approach involves a fixed image resolution while simultaneously integrating image descriptors from many FOVs corresponding to different sizes. For each study, the corresponding risk score (high scores reflecting aggressive disease and vice versa), predicted by a molecular assay (Oncotype DX), is available and serves as the surrogate ground truth for long-term patient outcome. Using the risk scores, a trained classifier is used to identify disease aggressiveness for each FOV size. The predictions for each FOV are then combined to yield the final prediction of disease aggressiveness (good, intermediate, or poor outcome). Independent multi-FOV classifiers are constructed for (1) 50 image features describing the spatial arrangement of cancer nuclei (via Voronoi diagram, Delaunay triangulation, and minimum spanning tree graphs) in H and E stained histopathology and (2) one image feature describing the vascular density in CD34 IHC stained histopathology. In a cohort of 29 patients, the multi-FOV classifiers obtained by combining information from the H and E and CD34 IHC stained channels were able to distinguish low- and high-risk patients with an accuracy of 0.91 &#177; 0.02 and a positive predictive value of 0.94 &#177; 0.10, suggesting that a purely image-based assay could potentially replace more expensive molecular assays for making disease prognostic predictions.
      Citation: Journal of Pathology Informatics 2011 2(2):1-1
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92027
      Issue No: Vol. 2, No. 2 (2012)
       
  • Local isotropic phase symmetry measure for detection of beta cells and
           lymphocytes
    • Authors: Manohar Kuse, Yi-Fang Wang, Vinay Kalasannavar, Michael Khan, Nasir Rajpoot
      Pages: 2 - 2
      Abstract: Manohar Kuse, Yi-Fang Wang, Vinay Kalasannavar, Michael Khan, Nasir Rajpoot

      Journal of Pathology Informatics 2011 2(2):2-2

      Diabetes can be associated with a reduction in functional &#946; cell mass, which must be restored if the disease is to be cured or progress is to be arrested. To study the cell count, it is also necessary to determine the number of nuclei within the insulin stained area. It can take a single experimentalist several months to complete a single study of this kind, results of which may still be quite subjective. In this paper, we propose a framework based on a novel measure of local symmetry for detection of cells. The local isotropic phase symmetry measure (LIPSyM) is designed to give high values at or near the cell centers. We demonstrate the effectiveness of our algorithm for detection of two types of specific cells in histology images, cells in mouse pancreatic sections and lymphocytes in human breast tissue. Experimental results for these two problems show that our algorithm performs better than human experts for the former problem, and outperforms the best reported results for the latter.
      Citation: Journal of Pathology Informatics 2011 2(2):2-2
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92028
      Issue No: Vol. 2, No. 2 (2012)
       
  • Prostate cancer detection: Fusion of cytological and textural features
    • Authors: Kien Nguyen, Anil K Jain, Bikash Sabata
      Pages: 3 - 3
      Abstract: Kien Nguyen, Anil K Jain, Bikash Sabata

      Journal of Pathology Informatics 2011 2(2):3-3

      A computer-assisted system for histological prostate cancer diagnosis can assist pathologists in two stages: (i) to locate cancer regions in a large digitized tissue biopsy, and (ii) to assign Gleason grades to the regions detected in stage 1. Most previous studies on this topic have primarily addressed the second stage by classifying the preselected tissue regions. In this paper, we address the first stage by presenting a cancer detection approach for the whole slide tissue image. We propose a novel method to extract a cytological feature, namely the presence of cancer nuclei (nuclei with prominent nucleoli) in the tissue, and apply this feature to detect the cancer regions. Additionally, conventional image texture features which have been widely used in the literature are also considered. The performance comparison among the proposed cytological textural feature combination method, the texture-based method and the cytological feature-based method demonstrates the robustness of the extracted cytological feature. At a false positive rate of 6%, the proposed method is able to achieve a sensitivity of 78% on a dataset including six training images (each of which has approximately 4,000x7,000 pixels) and 1 1 whole-slide test images (each of which has approximately 5,000x23,000 pixels). All images are at 20X magnification.
      Citation: Journal of Pathology Informatics 2011 2(2):3-3
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92030
      Issue No: Vol. 2, No. 2 (2012)
       
  • Automatic annotation of histopathological images using a latent topic
           model based on non-negative matrix factorization
    • Authors: Angel Cruz-Roa, Gloria Díaz, Eduardo Romero, Fabio A González
      Pages: 4 - 4
      Abstract: Angel Cruz-Roa, Gloria Díaz, Eduardo Romero, Fabio A González

      Journal of Pathology Informatics 2011 2(2):4-4

      Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively.
      Citation: Journal of Pathology Informatics 2011 2(2):4-4
      PubDate: Thu,19 Jan 2012
      Issue No: Vol. 2, No. 2 (2012)
       
  • A fully automated approach to prostate biopsy segmentation based on
           level-set and mean filtering
    • Authors: Juan Vidal, Gloria Bueno, John Galeotti, Marcial García-Rojo, Fernanda Relea, Oscar Déniz
      Pages: 5 - 5
      Abstract: Juan Vidal, Gloria Bueno, John Galeotti, Marcial García-Rojo, Fernanda Relea, Oscar Déniz

      Journal of Pathology Informatics 2011 2(2):5-5

      With modern automated microscopes and digital cameras, pathologists no longer have to examine samples looking through microscope binoculars. Instead, the slide is digitized to an image, which can then be examined on a screen. This creates the possibility for computers to analyze the image. In this work, a fully automated approach to region of interest (ROI) segmentation in prostate biopsy images is proposed. This will allow the pathologists to focus on the most important areas of the image. The method proposed is based on level-set and mean filtering techniques for lumen centered expansion and cell density localization respectively. The novelty of the technique lies in the ability to detect complete ROIs, where a ROI is composed by the conjunction of three different structures, that is, lumen, cytoplasm, and cells, as well as regions with a high density of cells. The method is capable of dealing with full biopsies digitized at different magnifications. In this paper, results are shown with a set of 100 H and E slides, digitized at 5&#215;, and ranging from 12 MB to 500 MB. The tests carried out show an average specificity above 99% across the board and average sensitivities of 95% and 80%, respectively, for the lumen centered expansion and cell density localization. The algorithms were also tested with images at 10&#215; magnification (up to 1228 MB) obtaining similar results.
      Citation: Journal of Pathology Informatics 2011 2(2):5-5
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92032
      Issue No: Vol. 2, No. 2 (2012)
       
  • Feasibility analysis of high resolution tissue image registration using
           3-D synthetic data
    • Authors: Yachna Sharma, Richard A Moffitt, Todd H Stokes, Qaiser Chaudry, May D Wang
      Pages: 6 - 6
      Abstract: Yachna Sharma, Richard A Moffitt, Todd H Stokes, Qaiser Chaudry, May D Wang

      Journal of Pathology Informatics 2011 2(2):6-6

      Background: Registration of high-resolution tissue images is a critical step in the 3D analysis of protein expression. Because the distance between images (~4-5&#956;m thickness of a tissue section) is nearly the size of the objects of interest (~10-20&#956;m cancer cell nucleus), a given object is often not present in both of two adjacent images. Without consistent correspondence of objects between images, registration becomes a difficult task. This work assesses the feasibility of current registration techniques for such images. Methods: We generated high resolution synthetic 3-D image data sets emulating the constraints in real data. We applied multiple registration methods to the synthetic image data sets and assessed the registration performance of three techniques (i.e., mutual information (MI), kernel density estimate (KDE) method [1], and principal component analysis (PCA)) at various slice thicknesses (with increments of 1&#956;m) in order to quantify the limitations of each method. Results: Our analysis shows that PCA, when combined with the KDE method based on nuclei centers, aligns images corresponding to 5&#956;m thick sections with acceptable accuracy. We also note that registration error increases rapidly with increasing distance between images, and that the choice of feature points which are conserved between slices improves performance. Conclusions: We used simulation to help select appropriate features and methods for image registration by estimating best-case-scenario errors for given data constraints in histological images. The results of this study suggest that much of the difficulty of stained tissue registration can be reduced to the problem of accurately identifying feature points, such as the center of nuclei.
      Citation: Journal of Pathology Informatics 2011 2(2):6-6
      PubDate: Thu,19 Jan 2012
      Issue No: Vol. 2, No. 2 (2012)
       
  • Atlas-guided correction of brain histology distortion
    • Authors: Xi Qiu, Lin Shi, Tony Pridmore, Alain Pitiot, Defeng Wang
      Pages: 7 - 7
      Abstract: Xi Qiu, Lin Shi, Tony Pridmore, Alain Pitiot, Defeng Wang

      Journal of Pathology Informatics 2011 2(2):7-7

      Histological tissue preparation stages (e.g., cutting, sectioning, etc.) often introduce tissue distortions that prevent a smooth 3D reconstruction from being built. In this paper, we propose a method to correct histology distortions by running a piecewise registration scheme. It takes the information of several consecutive slices in a neighborhood into account. In order to achieve an accurate anatomic presentation, we run the method iteratively with the assistance from a pre-segmented brain atlas. The registration parameters are optimized to accommodate different brain sub-regions, e.g., cerebellum, hippocampus, etc. The results are evaluated by both visual and quantitative approaches. The proposed method has been proved to be robust enough for reconstructing an accurate and smooth mouse brain volume.
      Citation: Journal of Pathology Informatics 2011 2(2):7-7
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92038
      Issue No: Vol. 2, No. 2 (2012)
       
  • Global error minimization in image mosaicing using graph connectivity and
           its applications in microscopy
    • Authors: Parmeshwar Khurd, Leo Grady, Rafiou Oketokoun, Hari Sundar, Tejas Gajera, Summer Gibbs-Strauss, John V Frangioni, Ali Kamen
      Pages: 8 - 8
      Abstract: Parmeshwar Khurd, Leo Grady, Rafiou Oketokoun, Hari Sundar, Tejas Gajera, Summer Gibbs-Strauss, John V Frangioni, Ali Kamen

      Journal of Pathology Informatics 2011 2(2):8-8

      Several applications such as multiprojector displays and microscopy require the mosaicing of images (tiles) acquired by a camera as it traverses an unknown trajectory in 3D space. A homography relates the image coordinates of a point in each tile to those of a reference tile provided the 3D scene is planar. Our approach in such applications is to first perform pairwise alignment of the tiles that have imaged common regions in order to recover a homography relating the tile pair. We then find the global set of homographies relating each individual tile to a reference tile such that the homographies relating all tile pairs are kept as consistent as possible. Using these global homographies, one can generate a mosaic of the entire scene. We derive a general analytical solution for the global homographies by representing the pair-wise homographies on a connectivity graph. Our solution can accommodate imprecise prior information regarding the global homographies whenever such information is available. We also derive equations for the special case of translation estimation of an X-Y microscopy stage used in histology imaging and present examples of stitched microscopy slices of specimens obtained after radical prostatectomy or prostate biopsy. In addition, we demonstrate the superiority of our approach over tree-structured approaches for global error minimization.
      Citation: Journal of Pathology Informatics 2011 2(2):8-8
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92039
      Issue No: Vol. 2, No. 2 (2012)
       
  • Interactive registration of 2D histology and 3D CT data for assessment of
           radiofrequency ablation treatment
    • Authors: Matthias Seise, Tuomas Alhonnoro, Marina Kolesnik
      Pages: 9 - 9
      Abstract: Matthias Seise, Tuomas Alhonnoro, Marina Kolesnik

      Journal of Pathology Informatics 2011 2(2):9-9

      Histological investigation of a lesion induced by radiofrequency ablation (RFA) treatment provides ground-truth about the true lesion size, thus verifying the success or failure of the RFA treatment. This work presents a framework for registration of two-dimensional large-scale histological sections and three-dimensional CT data typically used to guide the RFA intervention. The focus is on the developed interactive methods for reconstruction of the histological volume data by fusion of histological and high-resolution CT (MicroCT) data and registration into CT data based on natural feature points. The framework is evaluated using RFA interventions in a porcine liver and applying medically relevant metrics. The results of registration are within clinically required precision targets; thus the developed methods are suitable for validation of the RFA treatment.
      Citation: Journal of Pathology Informatics 2011 2(2):9-9
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92036
      Issue No: Vol. 2, No. 2 (2012)
       
  • Biomechanical model-based deformable registration of MRI and
           histopathology for clinical prostatectomy
    • Authors: Navid Samavati, Deirdre M McGrath, Jenny Lee, Theodorus van der Kwast, Michael Jewett, Cynthia Ménard, Kristy K Brock
      Pages: 10 - 10
      Abstract: Navid Samavati, Deirdre M McGrath, Jenny Lee, Theodorus van der Kwast, Michael Jewett, Cynthia Ménard, Kristy K Brock

      Journal of Pathology Informatics 2011 2(2):10-10

      A biomechanical model-based deformable image registration incorporating specimen-specific changes in material properties is optimized and evaluated for correlating histology of clinical prostatectomy specimens with in vivo MRI. In this methodology, a three-step registration based on biomechanics calculates the transformations between histology and fixed, fixed and fresh, and fresh and in vivo states. A heterogeneous linear elastic material model is constructed based on magnetic resonance elastography (MRE) results. The ex vivo tissue MRE data provide specimen-specific information for the fresh and fixed tissue to account for the changes due to fixation. The accuracy of the algorithm was quantified by calculating the target registration error (TRE) by identifying naturally occurring anatomical points within the prostate in each image. TRE were improved with the deformable registration algorithm compared to rigid registration alone. The qualitative assessment also showed a good alignment between histology and MRI after the proposed deformable registration.
      Citation: Journal of Pathology Informatics 2011 2(2):10-10
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92035
      Issue No: Vol. 2, No. 2 (2012)
       
  • A comparison of sampling strategies for histological image analysis
    • Authors: André Homeyer, Andrea Schenk, Uta Dahmen, Olaf Dirsch, Hai Huang, Horst K Hahn
      Pages: 11 - 11
      Abstract: André Homeyer, Andrea Schenk, Uta Dahmen, Olaf Dirsch, Hai Huang, Horst K Hahn

      Journal of Pathology Informatics 2011 2(2):11-11

      Histological image analysis methods often employ machine-learning classifiers in order to adapt to the huge variability of histological images. To train these classifiers, the user must select samples of the relevant image objects. In the field of active learning, there has been much research on sampling strategies that exploit the uncertainty of the current classification in order to guide the user to maximally informative samples. Although these approaches have the potential to reduce the training effort and increase the classification accuracy, they are very rarely employed in practice. In this paper, we investigate the practical value of uncertainty sampling in the context of histological image analysis. To obtain practically meaningful results, we have devised an evaluation algorithm that simulates the way a human interacts with a user interface. The results show that uncertainty sampling outperforms common random or error sampling strategies by achieving more accurate classification results with a lower number of training images.
      Citation: Journal of Pathology Informatics 2011 2(2):11-11
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92034
      Issue No: Vol. 2, No. 2 (2012)
       
  • Learning histopathological patterns
    • Authors: Andreas Kårsnäs, Anders L Dahl, Rasmus Larsen
      Pages: 12 - 12
      Abstract: Andreas Kårsnäs, Anders L Dahl, Rasmus Larsen

      Journal of Pathology Informatics 2011 2(2):12-12

      Aims: The aim was to demonstrate a method for automated image analysis of immunohistochemically stained tissue samples for extracting features that correlate with patient disease. We address the problem of quantifying tumor tissue and segmenting and counting cell nuclei. Materials and Methods: Our method utilizes a flexible segmentation method based on sparse coding trained from representative image samples. Nuclei counting is based on a nucleus model that takes size, shape, and nucleus probability into account. Nuclei clustering and overlays are resolved using a gray-weighted distance transform. We obtain a probability measure for pixels belonging to a nucleus from our segmentation procedure. Experiments are carried out on two sets of immunohistochemically stained images - one set based on the estrogen receptor (ER) and the other on antigen KI-67. For the nuclei separation we have selected 207 ER image samples from 58 tissue micro array-cores corresponding to 58 patients and 136 KI-67 image samples also from 58 cores. The images are hand-annotated by marking the center position of each nucleus. For the ER data we have a total of 1006 nuclei and for the KI-67 we have 796 nuclei. Segmentation performance was evaluated in terms of missing nuclei, falsely detected nuclei, and multiple detections. The proposed method is compared to state-of-the-art Bayesian classification. Statistical analysis used: The performance of the proposed method and a state-of-the-art algorithm including variations thereof is compared using the Wilcoxon rank sum test. Results: For both the ER experiment and the KI-67 experiment the proposed method exhibits lower error rates than the state-of-the-art method. Total error rates were 4.8 % and 7.7 % in the two experiments, corresponding to an average of 0.23 and 0.45 errors per image, respectively. The Wilcoxon rank sum tests show statistically significant improvements over the state-of-the-art method. Conclusions: We have demonstrated a method and obtained good performance compared to state-of-the-art nuclei separation. The segmentation procedure is simple, highly flexible, and we demonstrate how it, in addition to the nuclei separation, can perform precise segmentation of cancerous tissue. The complexity of the segmentation procedure is linear in the image size and the nuclei separation is linear in the number of nuclei. Additionally the method can be parallelized to obtain high-speed computations.
      Citation: Journal of Pathology Informatics 2011 2(2):12-12
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92033
      Issue No: Vol. 2, No. 2 (2012)
       
  • Graphical processing unit implementation of an integrated shape-based
           active contour: Application to digital pathology
    • Authors: Sahirzeeshan Ali, Anant Madabhushi
      Pages: 13 - 13
      Abstract: Sahirzeeshan Ali, Anant Madabhushi

      Journal of Pathology Informatics 2011 2(2):13-13

      Commodity graphics hardware has become a cost-effective parallel platform to solve many general computational problems. In medical imaging and more so in digital pathology, segmentation of multiple structures on high-resolution images, is often a complex and computationally expensive task. Shape-based level set segmentation has recently emerged as a natural solution to segmenting overlapping and occluded objects. However the flexibility of the level set method has traditionally resulted in long computation times and therefore might have limited clinical utility. The processing times even for moderately sized images could run into several hours of computation time. Hence there is a clear need to accelerate these segmentations schemes. In this paper, we present a parallel implementation of a computationally heavy segmentation scheme on a graphical processing unit (GPU). The segmentation scheme incorporates level sets with shape priors to segment multiple overlapping nuclei from very large digital pathology images. We report a speedup of 19&#215; compared to multithreaded C and MATLAB-based implementations of the same scheme, albeit with slight reduction in accuracy. Our GPU-based segmentation scheme was rigorously and quantitatively evaluated for the problem of nuclei segmentation and overlap resolution on digitized histopathology images corresponding to breast and prostate biopsy tissue specimens.
      Citation: Journal of Pathology Informatics 2011 2(2):13-13
      PubDate: Thu,19 Jan 2012
      DOI: 10.4103/2153-3539.92029
      Issue No: Vol. 2, No. 2 (2012)
       
  • Barriers and facilitators to adoption of soft copy interpretation from the
           user perspective: Lessons learned from filmless radiology for slideless
           pathology
    • Authors: Emily S Patterson, Mike Rayo, Carolina Gill, Metin N Gurcan
      Pages: 1 - 1
      Abstract: Emily S Patterson, Mike Rayo, Carolina Gill, Metin N Gurcan

      Journal of Pathology Informatics 2011 2(1):1-1

      Background: Adoption of digital images for pathological specimens has been slower than adoption of digital images in radiology, despite a number of anticipated advantages for digital images in pathology. In this paper, we explore the factors that might explain this slower rate of adoption. Materials and Method: Semi-structured interviews on barriers and facilitators to the adoption of digital images were conducted with two radiologists, three pathologists, and one pathologist's assistant. Results: Barriers and facilitators to adoption of digital images were reported in the areas of performance, workflow-efficiency, infrastructure, integration with other software, and exposure to digital images. The primary difference between the settings was that performance with the use of digital images as compared to the traditional method was perceived to be higher in radiology and lower in pathology. Additionally, exposure to digital images was higher in radiology than pathology, with some radiologists exclusively having been trained and/or practicing with digital images. The integration of digital images both improved and reduced efficiency in routine and non-routine workflow patterns in both settings, and was variable across the different organizations. A comparison of these findings with prior research on adoption of other health information technologies suggests that the barriers to adoption of digital images in pathology are relatively tractable. Conclusions: Improving performance using digital images in pathology would likely accelerate adoption of innovative technologies that are facilitated by the use of digital images, such as electronic imaging databases, electronic health records, double reading for challenging cases, and computer-aided diagnostic systems.
      Citation: Journal of Pathology Informatics 2011 2(1):1-1
      PubDate: Fri,7 Jan 2011
      DOI: 10.4103/2153-3539.74940
      Issue No: Vol. 2, No. 1 (2011)
       
  • Quantification of virtual slides: Approaches to analysis of content-based
           image information
    • Authors: Klaus Kayser
      Pages: 2 - 2
      Abstract: Klaus Kayser

      Journal of Pathology Informatics 2011 2(1):2-2

      Virtual microscopy, which is the diagnostic work on completely digitized histological and cytological slides as well as blood smears, is at the stage to be implemented in routine diagnostic surgical pathology (tissue-based diagnosis) in the near future, once it has been accepted by the US Food and Drug Administration. The principle of content-based image information, its mandatory prerequisites to obtain reproducible and stable image information as well as the different compartments that contribute to image information are described in detail. Automated extraction of content-based image information requires shading correction, constant maximum of grey values, and standardized grey value histograms. The different compartments to evaluate image information include objects, structure, and texture. Identification of objects and derived structure depend on segmentation accuracy and applied procedures; textures contain pixel-based image information only. All together, these image compartments posses the discrimination power to distinguish between object space and background, and, in addition, to reproducibly define regions of interest (ROIs). ROIs are image areas which display the information that is of preferable interest to the viewing pathologist. They contribute to the derived diagnosis to a higher level when compared with other image areas. The implementation of content-based image information algorithms to be applied for predictive tissue-based diagnoses is described in detail.
      Citation: Journal of Pathology Informatics 2011 2(1):2-2
      PubDate: Fri,7 Jan 2011
      DOI: 10.4103/2153-3539.74945
      Issue No: Vol. 2, No. 1 (2011)
       
  • Contemporary issues in transfusion medicine informatics
    • Authors: Gaurav Sharma, Anil V Parwani, Jay S Raval, Darrell J Triulzi, Richard J Benjamin, Liron Pantanowitz
      Pages: 3 - 3
      Abstract: Gaurav Sharma, Anil V Parwani, Jay S Raval, Darrell J Triulzi, Richard J Benjamin, Liron Pantanowitz

      Journal of Pathology Informatics 2011 2(1):3-3

      The Transfusion Medicine Service (TMS) covers diverse clinical and laboratory-based services that must be delivered with accuracy, efficiency and reliability. TMS oversight is shared by multiple regulatory agencies that cover product manufacturing and validation standards geared toward patient safety. These demands present significant informatics challenges. Over the past few decades, TMS information systems have improved to better handle blood product manufacturing, inventory, delivery, tracking and documentation. Audit trails and access to electronic databases have greatly facilitated product traceability and biovigilance efforts. Modern blood bank computing has enabled novel applications such as the electronic crossmatch, kiosk-based blood product delivery systems, and self-administered computerized blood donor interview and eligibility determination. With increasing use of barcoding technology, there has been a marked improvement in patient and specimen identification. Moreover, the emergence of national and international labeling standards such as ISBT 128 have facilitated the availability, movement and tracking of blood products across national and international boundaries. TMS has only recently begun to leverage the electronic medical record to address quality issues in transfusion practice and promote standardized documentation within institutions. With improved technology, future growth is expected in blood bank automation and product labeling with applications such as radio frequency identification devices. This article reviews several of these key informatics issues relevant to the contemporary practice of TMS.
      Citation: Journal of Pathology Informatics 2011 2(1):3-3
      PubDate: Fri,7 Jan 2011
      DOI: 10.4103/2153-3539.74961
      Issue No: Vol. 2, No. 1 (2011)
       
  • The 13 th world congress on medical and health informatics, Cape Town,
           South Africa: Partnerships for effective e-Health solutions
    • Authors: Andrew Georgiou
      Pages: 4 - 4
      Abstract: Andrew Georgiou

      Journal of Pathology Informatics 2011 2(1):4-4

      The 13 th World Congress on Medical and Health Informatics (Medinfo) was held in 2010 between 12 and 15 September in Cape Town, South Africa. This triennial international gathering is the official conference of the International Medical Informatics Association (IMIA) and brings together leading health informatics leaders, scientists, clinicians, researchers, vendors, developers and government and health care planners from around the globe. The conference attracted 905 submissions and resulted in a program that included 260 oral presentations, 349 posters presentations and 21 scientific demonstrations representing contributions from 58 countries. The Medinfo program covered all aspects of health informatics from traditional areas, such as hospital information systems, patient registries, nursing informatics, data integration, standards, interoperability issues and decision support, to innovative topics, such as translational bioinformatics, text mining, intelligent data analysis, emerging technologies, quality, social networking, workflow and organizational issues. The outgoing President of the IMIA, Professor Reinhold Haux, presented on health informatics challenges into the future, reinforcing that today and in the future, health care has to be considered as part of a continuous and coordinated life-time journey and not just as episodes of disease. Medical informatics has a key role to play in this paradigm shift. The new IMIA President, Professor Antoine Geissbuhler, was announced at the closing ceremony. The next Medinfo congress will take place in Copenhagen, Denmark, in September 2013.
      Citation: Journal of Pathology Informatics 2011 2(1):4-4
      PubDate: Sat,29 Jan 2011
      DOI: 10.4103/2153-3539.76152
      Issue No: Vol. 2, No. 1 (2011)
       
  • Informatics research using publicly available pathology data
    • Authors: Jules J Berman
      Pages: 5 - 5
      Abstract: Jules J Berman

      Journal of Pathology Informatics 2011 2(1):5-5

      The day has not arrived when pathology departments freely distribute their collected anatomic and clinical data for research purposes. Nonetheless, several valuable public domain data sets are currently available, from the U.S. Government. Two public data sets of special interest to pathologists are the SEER (the U.S. National Cancer Institute's Surveillance, Epidemiology and End Results program) public use data files, and the CDC (Center for Disease Control and Prevention) mortality files. The SEER files contain about 4 million de-identified cancer records, dating from 1973. The CDC mortality files contain approximately 85 million de-identified death records, dating from 1968. This editorial briefly describes both data sources, how they can be obtained, and how they may be used for pathology research.
      Citation: Journal of Pathology Informatics 2011 2(1):5-5
      PubDate: Sat,29 Jan 2011
      DOI: 10.4103/2153-3539.76154
      Issue No: Vol. 2, No. 1 (2011)
       
  • Virtual blood bank
    • Authors: Kit Fai Wong
      Pages: 6 - 6
      Abstract: Kit Fai Wong

      Journal of Pathology Informatics 2011 2(1):6-6

      Virtual blood bank is the computer-controlled, electronically linked information management system that allows online ordering and real-time, remote delivery of blood for transfusion. It connects the site of testing to the point of care at a remote site in a real-time fashion with networked computers thus maintaining the integrity of immunohematology test results. It has taken the advantages of information and communication technologies to ensure the accuracy of patient, specimen and blood component identification and to enhance personnel traceability and system security. The built-in logics and process constraints in the design of the virtual blood bank can guide the selection of appropriate blood and minimize transfusion risk. The quality of blood inventory is ascertained and monitored, and an audit trail for critical procedures in the transfusion process is provided by the paperless system. Thus, the virtual blood bank can help ensure that the right patient receives the right amount of the right blood component at the right time.
      Citation: Journal of Pathology Informatics 2011 2(1):6-6
      PubDate: Sat,29 Jan 2011
      DOI: 10.4103/2153-3539.76155
      Issue No: Vol. 2, No. 1 (2011)
       
  • "Meaningful use" of electronic health records and its relevance
           to laboratories and pathologists
    • Authors: Walter H Henricks
      Pages: 7 - 7
      Abstract: Walter H Henricks

      Journal of Pathology Informatics 2011 2(1):7-7

      Electronic health records (EHRs) have emerged as a major topic in health care and are central to the federal government's strategy for transforming healthcare delivery in the United States. Recent federal actions that aim to promote the use of EHRs promise to have significant implications for laboratories and for pathology practices. Under the HITECH (Health Information Technology Economic and Clinical Health) Act, an EHR incentive program has been established through which individual physicians and hospitals can qualify to receive incentive payments if they achieve "meaningful use" of "certified" EHR technology. The rule also establishes payment penalties in future years for eligible providers who have not met the requirements for meaningful use of EHRs. Meaningful use must be achieved using EHR technology that has been certified in accordance with functional and technical criteria that are set forth a regulation that parallels the meaningful use criteria in the incentive program. These actions and regulations are important to laboratories and pathologists for a number of reasons. Several of the criteria and requirements in the meaningful use rules and EHR certification criteria relate directly or indirectly to laboratory testing and laboratory information management, and future stage requirements are expected to impact the laboratory as well. Furthermore, as EHR uptake expands, there will be greater expectations for electronic interchange of laboratory information and laboratory information system (LIS)-EHR interfaces. Laboratories will need to be aware of the technical, operational, and business challenges that they may face as expectations for LIS-EHR increase. This paper reviews the important recent federal efforts aimed at accelerating EHR use, including the incentive program for EHR meaningful use, provider eligibility, and EHR certification criteria, from a perspective of their relevance for laboratories and pathology practices.
      Citation: Journal of Pathology Informatics 2011 2(1):7-7
      PubDate: Sat,12 Feb 2011
      DOI: 10.4103/2153-3539.76733
      Issue No: Vol. 2, No. 1 (2011)
       
  • Re: Barriers and facilitators to adoption of soft copy interpretation from
           the user perspective: Lessons learned from filmless radiology for
           slideless pathology. J Pathol Inform, 2011;2:1, Patterson et al.
    • Authors: Andrew J Evans
      Pages: 8 - 8
      Abstract: Andrew J Evans

      Journal of Pathology Informatics 2011 2(1):8-8


      Citation: Journal of Pathology Informatics 2011 2(1):8-8
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77170
      Issue No: Vol. 2, No. 1 (2011)
       
  • Barriers and facilitators to adoption of soft-copy interpretation from the
           user perspective: A comment
    • Authors: Viroj Wiwanitkit
      Pages: 9 - 9
      Abstract: Viroj Wiwanitkit

      Journal of Pathology Informatics 2011 2(1):9-9


      Citation: Journal of Pathology Informatics 2011 2(1):9-9
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77171
      Issue No: Vol. 2, No. 1 (2011)
       
  • Authors' Reply
    • Authors: Emily S Patterson, Mike Rayo, Carolina Gill, Metin N Gurcan
      Pages: 10 - 10
      Abstract: Emily S Patterson, Mike Rayo, Carolina Gill, Metin N Gurcan

      Journal of Pathology Informatics 2011 2(1):10-10


      Citation: Journal of Pathology Informatics 2011 2(1):10-10
      PubDate: Sat,26 Feb 2011
      Issue No: Vol. 2, No. 1 (2011)
       
  • Pathologists in a Net-Savvy World
    • Authors: Rashmi Patnayak, Amitabh Jena, Amit kumar Chowhan, N Rukamangadha, BV Phaneendra
      Pages: 11 - 11
      Abstract: Rashmi Patnayak, Amitabh Jena, Amit kumar Chowhan, N Rukamangadha, BV Phaneendra

      Journal of Pathology Informatics 2011 2(1):11-11


      Citation: Journal of Pathology Informatics 2011 2(1):11-11
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77173
      Issue No: Vol. 2, No. 1 (2011)
       
  • The pathologist is not a lonely sailor on the sea
    • Authors: Claudia Mello-Thoms
      Pages: 12 - 12
      Abstract: Claudia Mello-Thoms

      Journal of Pathology Informatics 2011 2(1):12-12


      Citation: Journal of Pathology Informatics 2011 2(1):12-12
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77174
      Issue No: Vol. 2, No. 1 (2011)
       
  • Spatially Invariant Vector Quantization: A pattern matching algorithm for
           multiple classes of image subject matter including pathology
    • Authors: Jason D Hipp, Jerome Y Cheng, Mehmet Toner, Ronald G Tompkins, Ulysses J Balis
      Pages: 13 - 13
      Abstract: Jason D Hipp, Jerome Y Cheng, Mehmet Toner, Ronald G Tompkins, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):13-13

      Introduction: Historically, effective clinical utilization of image analysis and pattern recognition algorithms in pathology has been hampered by two critical limitations: 1) the availability of digital whole slide imagery data sets and 2) a relative domain knowledge deficit in terms of application of such algorithms, on the part of practicing pathologists. With the advent of the recent and rapid adoption of whole slide imaging solutions, the former limitation has been largely resolved. However, with the expectation that it is unlikely for the general cohort of contemporary pathologists to gain advanced image analysis skills in the short term, the latter problem remains, thus underscoring the need for a class of algorithm that has the concurrent properties of image domain (or organ system) independence and extreme ease of use, without the need for specialized training or expertise. Results: In this report, we present a novel, general case pattern recognition algorithm, Spatially Invariant Vector Quantization (SIVQ), that overcomes the aforementioned knowledge deficit. Fundamentally based on conventional Vector Quantization (VQ) pattern recognition approaches, SIVQ gains its superior performance and essentially zero-training workflow model from its use of ring vectors, which exhibit continuous symmetry, as opposed to square or rectangular vectors, which do not. By use of the stochastic matching properties inherent in continuous symmetry, a single ring vector can exhibit as much as a millionfold improvement in matching possibilities, as opposed to conventional VQ vectors. SIVQ was utilized to demonstrate rapid and highly precise pattern recognition capability in a broad range of gross and microscopic use-case settings. Conclusion: With the performance of SIVQ observed thus far, we find evidence that indeed there exist classes of image analysis/pattern recognition algorithms suitable for deployment in settings where pathologists alone can effectively incorporate their use into clinical workflow, as a turnkey solution. We anticipate that SIVQ, and other related class-independent pattern recognition algorithms, will become part of the overall armamentarium of digital image analysis approaches that are immediately available to practicing pathologists, without the need for the immediate availability of an image analysis expert.
      Citation: Journal of Pathology Informatics 2011 2(1):13-13
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77175
      Issue No: Vol. 2, No. 1 (2011)
       
  • Development and implementation of an electronic interface for complex
           clinical laboratory instruments without a vendor-provided data transfer
           interface
    • Authors: Gary E Blank, Mohamed A Virji
      Pages: 14 - 14
      Abstract: Gary E Blank, Mohamed A Virji

      Journal of Pathology Informatics 2011 2(1):14-14

      Background: Clinical pathology laboratories increasingly use complex instruments that incorporate chromatographic separation, e.g. liquid chromatography, with mass detection for rapid identification and quantification of biochemicals, biomolecules, or pharmaceuticals. Electronic data management for these instruments through interfaces with laboratory information systems (LIS) is not generally available from the instrument manufacturers or LIS vendors. Unavailability of a data management interface is a limiting factor in the use of these instruments in clinical laboratories where there is a demand for high-throughput assays with turn-around times that meet patient care needs. Materials and Methods: Professional society guidelines for design and transfer of data between instruments and LIS were used in the development and implementation of the interface. File transfer protocols and support utilities were written to facilitate transfer of information between the instruments and the LIS. An interface was created for liquid chromatography-tandem mass spectroscopy and inductively coupled plasma-mass spectroscopy instruments to manage data in the Sunquest&#174; LIS. Results: Interface validation, implementation and data transfer fidelity as well as training of technologists for use of the interface was performed by the LIS group. The technologists were familiarized with the data verification process as a part of the data management protocol. The total time for the technologists for patient/control sample data entry, assay results data transfer, and results verification was reduced from approximately 20 s per sample to
      Citation: Journal of Pathology Informatics 2011 2(1):14-14
      PubDate: Sat,26 Feb 2011
      DOI: 10.4103/2153-3539.77176
      Issue No: Vol. 2, No. 1 (2011)
       
  • The tissue microarray data exchange specification: Extending TMA DES to
           provide flexible scoring and incorporate virtual slides
    • Authors: Alexander Wright, Oliver Lyttleton, Paul Lewis, Philip Quirke, Darren Treanor
      Pages: 15 - 15
      Abstract: Alexander Wright, Oliver Lyttleton, Paul Lewis, Philip Quirke, Darren Treanor

      Journal of Pathology Informatics 2011 2(1):15-15

      Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data.
      Citation: Journal of Pathology Informatics 2011 2(1):15-15
      PubDate: Tue,15 Mar 2011
      DOI: 10.4103/2153-3539.78038
      Issue No: Vol. 2, No. 1 (2011)
       
  • Web-based synoptic reporting for cancer checklists
    • Authors: Brett W Baskovich, Robert W Allan
      Pages: 16 - 16
      Abstract: Brett W Baskovich, Robert W Allan

      Journal of Pathology Informatics 2011 2(1):16-16

      Background: The surgical pathology report remains the primary source for information to guide the treatment of patients with cancer. Failure to report critical elements in a cancer report is an increasing problem in pathology because of the heightened complexity of these reports and number of elements that are important for patient care. The American College of Surgeons Commission on Cancer (ACS-CoC) in concert with the College of American Pathologists (CAP) developed checklists that contain all of the scientifically validated data elements that are to be reported for cancer specimens. Most institutions do not as of yet have pathology information systems in which CAP checklists are embedded into the laboratory information system (LIS). Entering the required elements often requires extensive text editing, secretarial support and deletion of extraneous elements that can be an arduous task. Materials and Methods: We sought to develop a web-based system that was available throughout the workstations in our department and was capable of generating synoptic reports based on the CAP guidelines. The program was written in a manner that allowed automatic generation of the web-based checklists through a parsing algorithm. Results: Multiple web-based synoptic report generators have been developed to encompass required elements of cancer synoptic reports as required by the ACS-CoC/ CAP. In addition, utilizing the same program, report generators for certain molecular tests (KRAS mutation) and FISH studies (UroVysion tm ) have also been developed. The output of these reports can be cut-and-pasted into any text-based anatomic pathology LIS. In addition, the elements can be compiled in a database. Conclusions: We describe a simple method to automate the development of web-based synoptic reports that can be entered into the anatomic pathology LIS and database.
      Citation: Journal of Pathology Informatics 2011 2(1):16-16
      PubDate: Tue,15 Mar 2011
      DOI: 10.4103/2153-3539.78039
      Issue No: Vol. 2, No. 1 (2011)
       
  • Extending the tissue microarray data exchange specification for inclusion
           of data analysis results
    • Authors: Oliver Lyttleton, Alexander Wright, Darren Treanor, Philip Quirke, Paul Lewis
      Pages: 17 - 17
      Abstract: Oliver Lyttleton, Alexander Wright, Darren Treanor, Philip Quirke, Paul Lewis

      Journal of Pathology Informatics 2011 2(1):17-17

      Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an eXtensible Markup Language (XML) specification for encoding TMA experiment data in a machine-readable format that is also human readable. TMA DES defines Common Data Elements (CDEs) that form a basic vocabulary for describing TMA data. TMA data are routinely subjected to univariate and multivariate statistical analysis to determine differences or similarities between pathologically distinct groups of tumors for one or more markers or between markers for different groups. Such statistical analysis tests include the t-test, ANOVA, Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. All these generate output that needs to be recorded and stored with TMA data. Materials and Methods: We propose extending the TMA DES to include syntactic and semantic definitions of CDEs for describing the results of statistical analyses performed upon TMA DES data. These CDEs are described in this paper and it is illustrated how they can be added to the TMA DES. We created a Document Type Definition (DTD) file defining the syntax for these CDEs, and a set of ISO 11179 entries providing semantic definitions for them. We describe how we wrote a program in R that read TMA DES data from an XML file, performed statistical analyses on that data, and created a new XML file containing both the original XML data and CDEs representing the results of our analyses. This XML file was submitted to XML parsers in order to confirm that they conformed to the syntax defined in our extended DTD file. TMA DES XML files with deliberately introduced errors were also parsed in order to verify that our new DTD file could perform error checking. Finally, we also validated an existing TMA DES XML file against our DTD file in order to demonstrate the backward compatibility of our DTD. Results: Our experiments demonstrated the encoding of analysis results using our proposed CDEs. We used XML parsers to confirm that these XML data were syntactically correct and conformed to the rules specified in our extended TMA DES DTD. We also demonstrated that this extended DTD was capable of being used to successfully perform error checking, and was backward compatible with pre-existing TMA DES data which did not use our new CDEs. Conclusions: The TMA DES allows Tissue Microarray data to be shared. A variety of statistical tests are used to analyze such data. We have proposed a set of CDEs as an extension to the TMA DES which can be used to annotate TMA DES data with the results of statistical analyses performed on that data. We performed experiments which demonstrated the usage of TMA DES data containing our proposed CDEs.
      Citation: Journal of Pathology Informatics 2011 2(1):17-17
      PubDate: Thu,31 Mar 2011
      DOI: 10.4103/2153-3539.78263
      Issue No: Vol. 2, No. 1 (2011)
       
  • Post-Informatics pathology
    • Authors: Jules J Berman
      Pages: 18 - 18
      Abstract: Jules J Berman

      Journal of Pathology Informatics 2011 2(1):18-18


      Citation: Journal of Pathology Informatics 2011 2(1):18-18
      PubDate: Thu,31 Mar 2011
      DOI: 10.4103/2153-3539.78499
      Issue No: Vol. 2, No. 1 (2011)
       
  • SIVQ-aided laser capture microdissection: A tool for high-throughput
           expression profiling
    • Authors: Jason Hipp, Jerome Cheng, Jeffrey C Hanson, Wusheng Yan, Phil Taylor, Nan Hu, Jaime Rodriguez-Canales, Jennifer Hipp, Michael A Tangrea, Michael R Emmert-Buck, Ulysses Balis
      Pages: 19 - 19
      Abstract: Jason Hipp, Jerome Cheng, Jeffrey C Hanson, Wusheng Yan, Phil Taylor, Nan Hu, Jaime Rodriguez-Canales, Jennifer Hipp, Michael A Tangrea, Michael R Emmert-Buck, Ulysses Balis

      Journal of Pathology Informatics 2011 2(1):19-19

      Introduction: Laser capture microdissection (LCM) facilitates procurement of defined cell populations for study in the context of histopathology. The morphologic assessment step in the LCM procedure is time consuming and tedious, thus restricting the utility of the technology for large applications. Results: Here, we describe the use of Spatially Invariant Vector Quantization (SIVQ) for histological analysis and LCM. Using SIVQ, we selected vectors as morphologic predicates that were representative of normal epithelial or cancer cells and then searched for phenotypically similar cells across entire tissue sections. The selected cells were subsequently auto-microdissected and the recovered RNA was analyzed by expression microarray. Gene expression profiles from SIVQ-LCM and standard LCM-derived samples demonstrated highly congruous signatures, confirming the equivalence of the differing microdissection methods. Conclusion: SIVQ-LCM improves the work-flow of microdissection in two significant ways. First, the process is transformative in that it shifts the pathologist's role from technical execution of the entire microdissection to a limited-contact supervisory role, enabling large-scale extraction of tissue by expediting subsequent semi-autonomous identification of target cell populations. Second, this work-flow model provides an opportunity to systematically identify highly constrained cell populations and morphologically consistent regions within tissue sections. Integrating SIVQ with LCM in a single environment provides advanced capabilities for efficient and high-throughput histological-based molecular studies.
      Citation: Journal of Pathology Informatics 2011 2(1):19-19
      PubDate: Thu,31 Mar 2011
      DOI: 10.4103/2153-3539.78500
      Issue No: Vol. 2, No. 1 (2011)
       
  • Global manipulation of digital images can lead to variation in cytological
           diagnosis
    • Authors: H Prasad, Sangeeta Wanjari, Rajkumar Parwani
      Pages: 20 - 20
      Abstract: H Prasad, Sangeeta Wanjari, Rajkumar Parwani

      Journal of Pathology Informatics 2011 2(1):20-20

      Background: With the adoption of a completely electronic workflow by several journals and the advent of telepathology, digital imaging has become an integral part of every scientific research. However, manipulating digital images is very easy, and it can lead to misinterpretations. Aim: To analyse the impact of manipulating digital images on their diagnosis. Design: Digital images were obtained from Papanicolaou-stained smears of dysplastic and normal oral epithelium. They were manipulated using GNU Image Manipulation Program (GIMP) to alter their brightness and contrast and color levels. A Power Point presentation composed of slides of these manipulated images along with the unaltered originals arranged randomly was created. The presentation was shown to five observers individually who rated the images as normal, mild, moderate or severe dysplasia. Weighted k statistics was used to measure and assess the levels of agreement between observers. Results: Levels of agreement between manipulated images and original images varied greatly among observers. Variation in diagnosis was in the form of overdiagnosis or under-diagnosis, usually by one grade. Conclusion: Global manipulations of digital images of cytological slides can significantly affect their interpretation. Such manipulations should therefore be kept to a minimum, and avoided wherever possible.
      Citation: Journal of Pathology Informatics 2011 2(1):20-20
      PubDate: Thu,31 Mar 2011
      DOI: 10.4103/2153-3539.78498
      Issue No: Vol. 2, No. 1 (2011)
       
  • Interinstitutional and interstate teleneuropathology
    • Authors: Clayton A Wiley, Geoff Murdoch, Anil Parwani, Terry Cudahy, David Wilson, Troy Payner, Kim Springer, Terrence Lewis
      Pages: 21 - 21
      Abstract: Clayton A Wiley, Geoff Murdoch, Anil Parwani, Terry Cudahy, David Wilson, Troy Payner, Kim Springer, Terrence Lewis

      Journal of Pathology Informatics 2011 2(1):21-21

      Background: Telemedicine has emerged as an efficient means of distributing professional medical expertise over a broad geographic area with few limitations to the various services that can be provided around the globe. Telepathology is particularly well suited to distributing subspecialty expertise in certain environments in an economical fashion, while preserving centers of excellence. Materials and Methods: After a decade of intrainstitutional teleneuropathology for intraoperative consultation, we expanded our practice to cross state lines and communicate between geographically and financially separate medical centers. Results: The result was an effective means of distributing neuropathological expertise while at the same time preserving a professional center of excellence. While technical and legal (i.e., physician licensing) barriers were surmounted, expected and unexpected issues related to communication required commitment on the part of multiple individuals with diverse expertise and responsibilities. Conclusion: Lessons learned from this successful venture can be used to facilitate future efforts in this ever-growing practical vehicle for distributing pathology subspecialty expertise.
      Citation: Journal of Pathology Informatics 2011 2(1):21-21
      PubDate: Wed,11 May 2011
      DOI: 10.4103/2153-3539.80717
      Issue No: Vol. 2, No. 1 (2011)
       
  • Reducing patient identification errors related to glucose point-of-care
           testing
    • Authors: Gaurav Alreja, Namrata Setia, James Nichols, Liron Pantanowitz
      Pages: 22 - 22
      Abstract: Gaurav Alreja, Namrata Setia, James Nichols, Liron Pantanowitz

      Journal of Pathology Informatics 2011 2(1):22-22

      Background: Patient identification (ID) errors in point-of-care testing (POCT) can cause test results to be transferred to the wrong patient's chart or prevent results from being transmitted and reported. Despite the implementation of patient barcoding and ongoing operator training at our institution, patient ID errors still occur with glucose POCT. The aim of this study was to develop a solution to reduce identification errors with POCT. Materials and Methods: Glucose POCT was performed by approximately 2,400 clinical operators throughout our health system. Patients are identified by scanning in wristband barcodes or by manual data entry using portable glucose meters. Meters are docked to upload data to a database server which then transmits data to any medical record matching the financial number of the test result. With a new model, meters connect to an interface manager where the patient ID (a nine-digit account number) is checked against patient registration data from admission, discharge, and transfer (ADT) feeds and only matched results are transferred to the patient's electronic medical record. With the new process, the patient ID is checked prior to testing, and testing is prevented until ID errors are resolved. Results: When averaged over a period of a month, ID errors were reduced to 3 errors/month (0.015%) in comparison with 61.5 errors/month (0.319%) before implementing the new meters. Conclusion: Patient ID errors may occur with glucose POCT despite patient barcoding. The verification of patient identification should ideally take place at the bedside before testing occurs so that the errors can be addressed in real time. The introduction of an ADT feed directly to glucose meters reduced patient ID errors in POCT.
      Citation: Journal of Pathology Informatics 2011 2(1):22-22
      PubDate: Wed,11 May 2011
      DOI: 10.4103/2153-3539.80718
      Issue No: Vol. 2, No. 1 (2011)
       
  • Standardization in digital pathology: Supplement 145 of the DICOM
           standards
    • Authors: Rajendra Singh, Lauren Chubb, Liron Pantanowitz, Anil Parwani
      Pages: 23 - 23
      Abstract: Rajendra Singh, Lauren Chubb, Liron Pantanowitz, Anil Parwani

      Journal of Pathology Informatics 2011 2(1):23-23

      As digital slides need a lot of storage space, lack of a singular method to acquire and store these large, two-dimensional images has been a major stumbling block in the universal acceptance of this technology. The DICOMS Standard Committee Working Group 26 has put in a tremendous effort to standardize storage methods so that they are more in line with currently available PACS in most hospitals for storage of radiology images. A recent press release (Supplement 145) of these standards was hailed by one and all involved in the field of digital pathology as it will make it easier for hospitals to integrate digital pathology into their already established systems without adding too much overhead costs. Besides, it will enable different vendors developing the scanners to upgrade their products to storage systems that are common across all systems.
      Citation: Journal of Pathology Informatics 2011 2(1):23-23
      PubDate: Wed,11 May 2011
      DOI: 10.4103/2153-3539.80719
      Issue No: Vol. 2, No. 1 (2011)
       
  • Stepping across borders into the future of telepathology
    • Authors: Alexis B Carter
      Pages: 24 - 24
      Abstract: Alexis B Carter

      Journal of Pathology Informatics 2011 2(1):24-24


      Citation: Journal of Pathology Informatics 2011 2(1):24-24
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82049
      Issue No: Vol. 2, No. 1 (2011)
       
  • Computer aided diagnostic tools aim to empower rather than replace
           pathologists: Lessons learned from computational chess
    • Authors: Jason Hipp, Thomas Flotte, James Monaco, Jerome Cheng, Anant Madabhushi, Yukako Yagi, Jaime Rodriguez-Canales, Michael Emmert-Buck, Michael C Dugan, Stephen Hewitt, Mehmet Toner, Ronald G Tompkins, David Lucas, John R Gilbertson, Ulysses J Balis
      Pages: 25 - 25
      Abstract: Jason Hipp, Thomas Flotte, James Monaco, Jerome Cheng, Anant Madabhushi, Yukako Yagi, Jaime Rodriguez-Canales, Michael Emmert-Buck, Michael C Dugan, Stephen Hewitt, Mehmet Toner, Ronald G Tompkins, David Lucas, John R Gilbertson, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):25-25


      Citation: Journal of Pathology Informatics 2011 2(1):25-25
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82050
      Issue No: Vol. 2, No. 1 (2011)
       
  • Why a pathology image should not be considered as a radiology image
    • Authors: Jason D Hipp, Anna Fernandez, Carolyn C Compton, Ulysses J Balis
      Pages: 26 - 26
      Abstract: Jason D Hipp, Anna Fernandez, Carolyn C Compton, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):26-26


      Citation: Journal of Pathology Informatics 2011 2(1):26-26
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82051
      Issue No: Vol. 2, No. 1 (2011)
       
  • Digital slides and ACGME resident competencies in anatomic pathology: An
           altered paradigm for acquisition and assessment
    • Authors: Lewis A Hassell, Kar-Ming Fung, Brad Chaser
      Pages: 27 - 27
      Abstract: Lewis A Hassell, Kar-Ming Fung, Brad Chaser

      Journal of Pathology Informatics 2011 2(1):27-27

      Whole slide digital imaging technology has matured considerably over the past decade. Applications in pathology education are widespread and are rapidly transforming the manner in which medical students learn pathology and histology, and they have a novel and significant impact on postgraduate continuing medical education. Whole slide digital images for use in pathology graduate education have been slower in adoption and remain much less widespread. Emphasis on professional competency by the Accreditation Council on Graduate Medical Education (ACGME) and credentialing organizations, however, appear poised to significantly increase. The convergence of these two forces is propitious for pathology training. This article examines the opportunities for the use of whole slide images (WSI) in pathology residency training along with the developing potential uses in each of the areas of competency, as categorized by the ACGME. Barriers to WSI adoption in the pathology community are identified along with potentially significant promoters for adoption in training and practice. Current literature and recent presentations are reviewed. Digital pathology coupled with emphasis on competency is a shift of tremendous magnitude that can dramatically improve our abilities to help trainees acquire, demonstrate, and maintain the skills to practice pathology in the generation ahead.
      Citation: Journal of Pathology Informatics 2011 2(1):27-27
      PubDate: Tue,14 Jun 2011
      Issue No: Vol. 2, No. 1 (2011)
       
  • Modified full-field optical coherence tomography: A novel tool for rapid
           histology of tissues
    • Authors: Manu Jain, Nidhi Shukla, Maryem Manzoor, Sylvie Nadolny, Sushmita Mukherjee
      Pages: 28 - 28
      Abstract: Manu Jain, Nidhi Shukla, Maryem Manzoor, Sylvie Nadolny, Sushmita Mukherjee

      Journal of Pathology Informatics 2011 2(1):28-28

      Background: Here, we report the first use of a commercial prototype of full-field optical coherence tomography called Light-CT TM . Based on the principle of white light interferometry, Light-CT TM generates quick high-resolution three-dimensional tomographic images from unprocessed tissues. Its advantage over the current intra-surgical diagnostic standard, i.e. frozen section analysis, lies in the absence of freezing artifacts, which allows real-time diagnostic impressions, and/or for the tissues to be triaged for subsequent conventional histopathology. Materials and Methods: In this study, we recapitulate known normal histology in nine formalin fixed ex vivo rat organs (skin, heart, lung, liver, stomach, kidney, prostate, urinary bladder, and testis). Large surface and virtually sectioned stacks of images at varying depths were acquired by a pair of 10x/0.3 numerical aperture water immersion objectives, processed and visualized in real time. Results: Normal histology of the following organs was recapitulated by identifying various tissue microstructures. Skin: epidermis, dermal-epidermal junction and hair follicles with surrounding sebaceous glands in the dermis. Stomach: mucosa with surface pits, submucosa, muscularis propria and serosa. Liver: hepatocytes separated by sinusoidal spaces, central veins and portal triad. Kidney: convoluted tubules, medullary rays (straight tubules) and collecting ducts. Prostate: acini and fibro-muscular stroma. Lung: bronchi, bronchioles, alveolar ducts, alveoli and pleura. Urinary bladder: urothelium, lamina propria, muscularis propria, and serosa. Testis: seminiferous tubules with intra-tubular sperms. Conclusion: Light-CT TM is a powerful imaging tool to perform fast histology on fresh and fixed tissues, without introducing artifacts. Its compact size, ease of handling, fast image acquisition and safe incident light levels makes it well-suited for various intra-operative and intra-procedural triaging and decision making applications.
      Citation: Journal of Pathology Informatics 2011 2(1):28-28
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82053
      Issue No: Vol. 2, No. 1 (2011)
       
  • Comment on "Modified full-field optical coherence tomography: A novel
           tool for rapid histology of fresh tissues"
    • Authors: Jeffrey L Fine
      Pages: 29 - 29
      Abstract: Jeffrey L Fine

      Journal of Pathology Informatics 2011 2(1):29-29


      Citation: Journal of Pathology Informatics 2011 2(1):29-29
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82054
      Issue No: Vol. 2, No. 1 (2011)
       
  • University of Pittsburgh Medical Center remains tracker: A novel
           application for tracking decedents and improving the autopsy workflow
    • Authors: Matthew A Smith, Somak Roy, Rick Nestler, Beth Augustine, David Miller, Anil Parwani, Lawrence Nichols
      Pages: 30 - 30
      Abstract: Matthew A Smith, Somak Roy, Rick Nestler, Beth Augustine, David Miller, Anil Parwani, Lawrence Nichols

      Journal of Pathology Informatics 2011 2(1):30-30

      All hospitals deal with patient deaths. Multiple departments and personnel must be coordinated to ensure that decedents are safely managed. Prior to 2004, at the University of Pittsburgh Medical Center (UPMC), when a patient passed away, the process of alerting involved personnel, transporting the decedent, and tracking the completion of clinical documents was cumbersome and inefficient. In order to address these concerns, UPMC Remains Tracker, a web-based application, was developed to improve the efficiency and simplify the logistics related to the management of patient deaths. The UPMC Information Services division developed UPMC Remains Tracker, an application that tracks decedents' locations, documentation status, and autopsy status within UPMC hospitals. We assessed qualitative improvement in decedent remains tracking, decedent paperwork management, and staff satisfaction and compliance. UPMC Remains Tracker improved the process of tracking decedents' locations, identifying involved personnel, monitoring autopsy requests, and determining the availability for funeral home transportation. Resident satisfaction with UPMC Remains Tracker was generally positive and scored as "Improved efficiency" and makes identifying and tracking decedents "Much easier". Additionally, the nursing staff reacted favorably to the application. A retrospective review of the use of the application in the management of 100 decedents demonstrated a 93% compliance rate. Among the cases requiring an autopsy, there was a 90% compliance rate. The process of tracking decedents, their paperwork, involved staff, and decedent autopsy status is often inefficient. This assessment suggests that incorporating new technologies such as UPMC Remains Tracker into the management of hospital deaths provides accurate tracking of remains, streamlines the administrative tasks associated with deaths, and increases nursing and resident satisfaction and compliance.
      Citation: Journal of Pathology Informatics 2011 2(1):30-30
      PubDate: Tue,14 Jun 2011
      DOI: 10.4103/2153-3539.82055
      Issue No: Vol. 2, No. 1 (2011)
       
  • The need for the pathology community to sponsor a whole slide imaging
           repository with technical guidance from the pathology informatics
           community
    • Authors: Jason D Hipp, Jeffrey Sica, Barbara McKenna, James Monaco, Anant Madabhushi, Jerome Cheng, Ulysses J Balis
      Pages: 31 - 31
      Abstract: Jason D Hipp, Jeffrey Sica, Barbara McKenna, James Monaco, Anant Madabhushi, Jerome Cheng, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):31-31


      Citation: Journal of Pathology Informatics 2011 2(1):31-31
      PubDate: Tue,26 Jul 2011
      DOI: 10.4103/2153-3539.83191
      Issue No: Vol. 2, No. 1 (2011)
       
  • A data model and database for high-resolution pathology analytical image
           informatics
    • Authors: Fusheng Wang, Jun Kong, Lee Cooper, Tony Pan, Tahsin Kurc, Wenjin Chen, Ashish Sharma, Cristobal Niedermayr, Tae W Oh, Daniel Brat, Alton B Farris, David J Foran, Joel Saltz
      Pages: 32 - 32
      Abstract: Fusheng Wang, Jun Kong, Lee Cooper, Tony Pan, Tahsin Kurc, Wenjin Chen, Ashish Sharma, Cristobal Niedermayr, Tae W Oh, Daniel Brat, Alton B Farris, David J Foran, Joel Saltz

      Journal of Pathology Informatics 2011 2(1):32-32

      Background: The systematic analysis of imaged pathology specimens often results in a vast amount of morphological information at both the cellular and sub-cellular scales. While microscopy scanners and computerized analysis are capable of capturing and analyzing data rapidly, microscopy image data remain underutilized in research and clinical settings. One major obstacle which tends to reduce wider adoption of these new technologies throughout the clinical and scientific communities is the challenge of managing, querying, and integrating the vast amounts of data resulting from the analysis of large digital pathology datasets. This paper presents a data model, which addresses these challenges, and demonstrates its implementation in a relational database system. Context: This paper describes a data model, referred to as Pathology Analytic Imaging Standards (PAIS), and a database implementation, which are designed to support the data management and query requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines on whole-slide images and tissue microarrays (TMAs). Aims: (1) Development of a data model capable of efficiently representing and storing virtual slide related image, annotation, markup, and feature information. (2) Development of a database, based on the data model, capable of supporting queries for data retrieval based on analysis and image metadata, queries for comparison of results from different analyses, and spatial queries on segmented regions, features, and classified objects. Settings and Design: The work described in this paper is motivated by the challenges associated with characterization of micro-scale features for comparative and correlative analyses involving whole-slides tissue images and TMAs. Technologies for digitizing tissues have advanced significantly in the past decade. Slide scanners are capable of producing high-magnification, high-resolution images from whole slides and TMAs within several minutes. Hence, it is becoming increasingly feasible for basic, clinical, and translational research studies to produce thousands of whole-slide images. Systematic analysis of these large datasets requires efficient data management support for representing and indexing results from hundreds of interrelated analyses generating very large volumes of quantifications such as shape and texture and of classifications of the quantified features. Materials and Methods: We have designed a data model and a database to address the data management requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines. The data model represents virtual slide related image, annotation, markup and feature information. The database supports a wide range of metadata and spatial queries on images, annotations, markups, and features. Results: We currently have three databases running on a Dell PowerEdge T410 server with CentOS 5.5 Linux operating system. The database server is IBM DB2 Enterprise Edition 9.7.2. The set of databases consists of 1) a TMA database containing image analysis results from 4740 cases of breast cancer, with 641 MB storage size; 2) an algorithm validation database, which stores markups and annotations from two segmentation algorithms and two parameter sets on 18 selected slides, with 66 GB storage size; and 3) an in silico brain tumor study database comprising results from 307 TCGA slides, with 365 GB storage size. The latter two databases also contain human-generated annotations and markups for regions and nuclei. Conclusions: Modeling and managing pathology image analysis results in a database provide immediate benefits on the value and usability of data in a research study. The database provides powerful query capabilities, which are otherwise difficult or cumbersome to support by other approaches such as programming languages. Standardized, semantic annotated data representation and interfaces also make it possible to more efficiently share image data and analysis results.
      Citation: Journal of Pathology Informatics 2011 2(1):32-32
      PubDate: Tue,26 Jul 2011
      DOI: 10.4103/2153-3539.83192
      Issue No: Vol. 2, No. 1 (2011)
       
  • Computer-aided identification of prostatic adenocarcinoma: Segmentation of
           glandular structures
    • Authors: Yahui Peng, Yulei Jiang, Laurie Eisengart, Mark A Healy, Francis H Straus, Ximing J Yang
      Pages: 33 - 33
      Abstract: Yahui Peng, Yulei Jiang, Laurie Eisengart, Mark A Healy, Francis H Straus, Ximing J Yang

      Journal of Pathology Informatics 2011 2(1):33-33

      Background: Identification of individual prostatic glandular structures is an important prerequisite to quantitative histological analysis of prostate cancer with the aid of a computer. We have developed a computer method to segment individual glandular units and to extract quantitative image features, for computer identification of prostatic adenocarcinoma. Methods: Two sets of digital histology images were used: database I (n = 57) for developing and testing the computer technique, and database II (n = 116) for independent validation. The segmentation technique was based on a k-means clustering and a region-growing method. Computer segmentation results were evaluated subjectively and also compared quantitatively against manual gland outlines, using the Jaccard similarity measure. Quantitative features that were extracted from the computer segmentation results include average gland size, spatial gland density, and average gland circularity. Linear discriminant analysis (LDA) was used to combine quantitative image features. Classification performance was evaluated with receiver operating characteristic (ROC) analysis and the area under the ROC curve (AUC). Results: Jaccard similarity coefficients between computer segmentation and manual outlines of individual glands were between 0.63 and 0.72 for non-cancer and between 0.48 and 0.54 for malignant glands, respectively, similar to an interobserver agreement of 0.79 for non-cancer and 0.75 for malignant glands, respectively. The AUC value for the features of average gland size and gland density combined via LDA was 0.91 for database I and 0.96 for database II. Conclusions: Using a computer, we are able to delineate individual prostatic glands automatically and identify prostatic adenocarcinoma accurately, based on the quantitative image features extracted from computer-segmented glandular structures.
      Citation: Journal of Pathology Informatics 2011 2(1):33-33
      PubDate: Tue,26 Jul 2011
      DOI: 10.4103/2153-3539.83193
      Issue No: Vol. 2, No. 1 (2011)
       
  • A review of radio frequency identification technology for the anatomic
           pathology or biorepository laboratory: Much promise, some progress, and
           more work needed
    • Authors: Jerry J Lou, Gary Andrechak, Michael Riben, William H Yong
      Pages: 34 - 34
      Abstract: Jerry J Lou, Gary Andrechak, Michael Riben, William H Yong

      Journal of Pathology Informatics 2011 2(1):34-34

      Patient safety initiatives throughout the anatomic laboratory and in biorepository laboratories have mandated increasing emphasis on the need for accurately identifying and tracking biospecimen assets throughout their production lifecycle and for archiving/retrieval purposes. However, increasing production volume along with complex workflow characteristics, reliance on manual production processes, and required asset movement to disparate destinations throughout asset lifecycles continue to challenge laboratory efforts. Radio Frequency Identification (RFID) technology, use of radio waves to communicate data between electronic tags attached to objects and a reader, shows significant potential to facilitate and overcome these hurdles. Advantages over traditional barcode labeling include readability without direct line-of-sight alignment to the reader, ability to read multiple tags simultaneously, higher data storage capacity, faster data transmission rate, and capacity to perform multiple read-writes of data to the tag. Most importantly, use of radio waves decreases the need to manually scan each asset, and at each step, identification or tracking event is needed. Temperature monitoring by on-board sensors and three-dimensional position tracking are additional potential benefits of using RFID technology. To date, barriers to implementation of RFID systems in the anatomic laboratory include increased associated costs of tags and readers, system software, data security concerns, lack of specific data standards for stored information, and potential for technological obsolescence during decades of specimen storage. Novel RFID production techniques and increased production capacity are projected to lower costs of some tags to a few cents each. Potentially, information security concerns can be addressed by techniques such as shielding, data encryption, and tag pseudonyms. Commitment by stakeholder groups to develop RFID tag data standards for anatomic pathology and biorepository laboratories could avoid or mitigate the "islands of data" dilemma presented by barcode usage where there are innumerable standards and a consequent paucity of hardware or software "plug and play" interoperability. Work remains to be done to establish the durability and appropriate shielding of individual tag types for use in harsh laboratory environmental conditions, and for long-term archival storage. Finally, given the requirements for long-term storage of biospecimen assets, consideration should be given to ways of mitigating data isolation due to eventual technological obsolescence of a particular RFID technology or software.
      Citation: Journal of Pathology Informatics 2011 2(1):34-34
      PubDate: Sat,13 Aug 2011
      DOI: 10.4103/2153-3539.83738
      Issue No: Vol. 2, No. 1 (2011)
       
  • Computerized provider order entry in the clinical laboratory
    • Authors: Jason M Baron, Anand S Dighe
      Pages: 35 - 35
      Abstract: Jason M Baron, Anand S Dighe

      Journal of Pathology Informatics 2011 2(1):35-35

      Clinicians have traditionally ordered laboratory tests using paper-based orders and requisitions. However, paper orders are becoming increasingly incompatible with the complexities, challenges, and resource constraints of our modern healthcare systems and are being replaced by electronic order entry systems. Electronic systems that allow direct provider input of diagnostic testing or medication orders into a computer system are known as Computerized Provider Order Entry (CPOE) systems. Adoption of laboratory CPOE systems may offer institutions many benefits, including reduced test turnaround time, improved test utilization, and better adherence to practice guidelines. In this review, we outline the functionality of various CPOE implementations, review the reported benefits, and discuss strategies for using CPOE to improve the test ordering process. Further, we discuss barriers to the implementation of CPOE systems that have prevented their more widespread adoption.
      Citation: Journal of Pathology Informatics 2011 2(1):35-35
      PubDate: Sat,13 Aug 2011
      DOI: 10.4103/2153-3539.83740
      Issue No: Vol. 2, No. 1 (2011)
       
  • Review of the current state of whole slide imaging in pathology
    • Authors: Liron Pantanowitz, Paul N Valenstein, Andrew J Evans, Keith J Kaplan, John D Pfeifer, David C Wilbur, Laura C Collins, Terence J Colgan
      Pages: 36 - 36
      Abstract: Liron Pantanowitz, Paul N Valenstein, Andrew J Evans, Keith J Kaplan, John D Pfeifer, David C Wilbur, Laura C Collins, Terence J Colgan

      Journal of Pathology Informatics 2011 2(1):36-36

      Whole slide imaging (WSI), or "virtual" microscopy, involves the scanning (digitization) of glass slides to produce "digital slides". WSI has been advocated for diagnostic, educational and research purposes. When used for remote frozen section diagnosis, WSI requires a thorough implementation period coupled with trained support personnel. Adoption of WSI for rendering pathologic diagnoses on a routine basis has been shown to be successful in only a few "niche" applications. Wider adoption will most likely require full integration with the laboratory information system, continuous automated scanning, high-bandwidth connectivity, massive storage capacity, and more intuitive user interfaces. Nevertheless, WSI has been reported to enhance specific pathology practices, such as scanning slides received in consultation or of legal cases, of slides to be used for patient care conferences, for quality assurance purposes, to retain records of slides to be sent out or destroyed by ancillary testing, and for performing digital image analysis. In addition to technical issues, regulatory and validation requirements related to WSI have yet to be adequately addressed. Although limited validation studies have been published using WSI there are currently no standard guidelines for validating WSI for diagnostic use in the clinical laboratory. This review addresses the current status of WSI in pathology related to regulation and validation, the provision of remote and routine pathologic diagnoses, educational uses, implementation issues, and the cost-benefit analysis of adopting WSI in routine clinical practice.
      Citation: Journal of Pathology Informatics 2011 2(1):36-36
      PubDate: Sat,13 Aug 2011
      DOI: 10.4103/2153-3539.83746
      Issue No: Vol. 2, No. 1 (2011)
       
  • Automated vector selection of SIVQ and parallel computing integration
           MATLAB TM : Innovations supporting large-scale and high-throughput image
           analysis studies
    • Authors: Jerome Cheng, Jason Hipp, James Monaco, David R Lucas, Anant Madabhushi, Ulysses J Balis
      Pages: 37 - 37
      Abstract: Jerome Cheng, Jason Hipp, James Monaco, David R Lucas, Anant Madabhushi, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):37-37

      Introduction: Spatially invariant vector quantization (SIVQ) is a texture and color-based image matching algorithm that queries the image space through the use of ring vectors. In prior studies, the selection of one or more optimal vectors for a particular feature of interest required a manual process, with the user initially stochastically selecting candidate vectors and subsequently testing them upon other regions of the image to verify the vector's sensitivity and specificity properties (typically by reviewing a resultant heat map). In carrying out the prior efforts, the SIVQ algorithm was noted to exhibit highly scalable computational properties, where each region of analysis can take place independently of others, making a compelling case for the exploration of its deployment on high-throughput computing platforms, with the hypothesis that such an exercise will result in performance gains that scale linearly with increasing processor count. Methods: An automated process was developed for the selection of optimal ring vectors to serve as the predicate matching operator in defining histopathological features of interest. Briefly, candidate vectors were generated from every possible coordinate origin within a user-defined vector selection area (VSA) and subsequently compared against user-identified positive and negative "ground truth" regions on the same image. Each vector from the VSA was assessed for its goodness-of-fit to both the positive and negative areas via the use of the receiver operating characteristic (ROC) transfer function, with each assessment resulting in an associated area-under-the-curve (AUC) figure of merit. Results: Use of the above-mentioned automated vector selection process was demonstrated in two cases of use: First, to identify malignant colonic epithelium, and second, to identify soft tissue sarcoma. For both examples, a very satisfactory optimized vector was identified, as defined by the AUC metric. Finally, as an additional effort directed towards attaining high-throughput capability for the SIVQ algorithm, we demonstrated the successful incorporation of it with the MATrix LABoratory (MATLAB TM ) application interface. Conclusion: The SIVQ algorithm is suitable for automated vector selection settings and high throughput computation.
      Citation: Journal of Pathology Informatics 2011 2(1):37-37
      PubDate: Sat,13 Aug 2011
      DOI: 10.4103/2153-3539.83752
      Issue No: Vol. 2, No. 1 (2011)
       
  • The accuracy of dynamic predictive autofocusing for whole slide imaging
    • Authors: Richard R McKay, Vipul A Baxi, Michael C Montalto
      Pages: 38 - 38
      Abstract: Richard R McKay, Vipul A Baxi, Michael C Montalto

      Journal of Pathology Informatics 2011 2(1):38-38

      Context: Whole slide imaging (WSI) for digital pathology involves the rapid automated acquisition of multiple high-power fields from a microscope slide containing a tissue specimen. Capturing each field in the correct focal plane is essential to create high-quality digital images. Others have described a novel focusing method which reduces the number of focal planes required to generate accurate focus. However, this method was not applied dynamically in an automated WSI system under continuous motion. Aims: This report measures the accuracy of this method when applied in a rapid continuous scan mode using a dual sensor WSI system with interleaved acquisition of images. Methods: We acquired over 400 tiles in a "stop and go" scan mode, surveying the entire z depth in each tile and used this as ground truth. We compared this ground truth focal height to the focal height determined using a rapid 3-point focus algorithm applied dynamically in a continuous scanning mode. Results: Our data showed the average focal height error of 0.30 (&#177;0.27) &#956;m compared to ground truth, which is well within the system's depth of field. On a tile by tile assessment, approximately 95% of the tiles were within the system's depth of field. Further, this method was six times faster than acquiring tiles compared to the same method in a non-continuous scan mode. Conclusions: The data indicates that the method employed can yield a significant improvement in scan speed while maintaining highly accurate autofocusing.
      Citation: Journal of Pathology Informatics 2011 2(1):38-38
      PubDate: Wed,24 Aug 2011
      DOI: 10.4103/2153-3539.84231
      Issue No: Vol. 2, No. 1 (2011)
       
  • Implementation of whole slide imaging in surgical pathology: A value added
           approach
    • Authors: Mike Isaacs, Jochen K Lennerz, Stacey Yates, Walter Clermont, Joan Rossi, John D Pfeifer
      Pages: 39 - 39
      Abstract: Mike Isaacs, Jochen K Lennerz, Stacey Yates, Walter Clermont, Joan Rossi, John D Pfeifer

      Journal of Pathology Informatics 2011 2(1):39-39

      Background: Whole slide imaging (WSI) makes it possible to capture images of an entire histological slide. WSI has established roles in surgical pathology, including support of off-site frozen section interpretation, primary diagnosis, educational activities, and laboratory quality assurance (QA) activities. Analyses of the cost of WSI have traditionally been based solely on direct costs and diagnostic accuracy; however, these types of analyses largely ignore workflow and cost issues that arise as a result of redundancy, the need for additional staffing, and customized software development when WSI is integrated into routine diagnostic surgical pathology. The pre-scan, scan, and post-scan costs; quality control and QA costs; and IT process costs can be significant, and consequently, pathology groups can find it difficult to perform a realistic cost-benefit analysis of adding WSI to their practice. Materials and Methods: In this paper, we report a "value added" approach developed to guide our decisions regarding integration of WSI into surgical pathology practice. The approach focuses on specific operational measures (cost, time, and enhanced patient care) and practice settings (clinical, education, and research) to identify routine activities in which the addition of WSI can provide improvements. Results: When applied to our academic pathology group practice, the value added approach resulted in expanded and improved operations, as demonstrated by outcome based measures. Conclusion: A value added can be used to perform a realistic cost-benefit analysis of integrating WSI into routine surgical pathology practice.
      Citation: Journal of Pathology Informatics 2011 2(1):39-39
      PubDate: Wed,24 Aug 2011
      DOI: 10.4103/2153-3539.84232
      Issue No: Vol. 2, No. 1 (2011)
       
  • Using XML to encode TMA DES metadata
    • Authors: Oliver Lyttleton, Alexander Wright, Darren Treanor, Paul Lewis
      Pages: 40 - 40
      Abstract: Oliver Lyttleton, Alexander Wright, Darren Treanor, Paul Lewis

      Journal of Pathology Informatics 2011 2(1):40-40

      Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.
      Citation: Journal of Pathology Informatics 2011 2(1):40-40
      PubDate: Wed,24 Aug 2011
      DOI: 10.4103/2153-3539.84233
      Issue No: Vol. 2, No. 1 (2011)
       
  • Use of mobile high-resolution device for remote frozen section evaluation
           of whole slide images
    • Authors: Joel Ramey, Kar Ming Fung, Lewis A Hassell
      Pages: 41 - 41
      Abstract: Joel Ramey, Kar Ming Fung, Lewis A Hassell

      Journal of Pathology Informatics 2011 2(1):41-41

      Introduction: With recent advances, it is now possible to view whole slide images (WSI) on mobile, high-resolution, viewing devices (MVD). This creates a new paradigm in which MVDs may be used for consultation and/or diagnosis. Validation of the results with devices is important for practitioners and regulators. We evaluated the use of MVDs in frozen section (FS) interpretation. Methods: A series of 72 consecutive FS cases were selected for potential inclusion in the study. A 67 case subset of these were successfully scanned at 20x magnification. Scan times were recorded. A sample of WSI FS cases, with gross and clinical information, was presented to six pathologists on an iPad MVD using the Interpath application. Times to diagnosis were recorded. Results were compared with the original reported and final diagnosis. Participants also completed a survey assessing image quality, interface, and diagnostic comfort level. Results: Scan times averaged two minutes and 46 seconds per slide, (standard deviation [SD] 2 minutes 46 seconds). Evaluation times averaged 4 minutes and 59 seconds per case, range to 13 minutes and 50 seconds, SD 3 minutes 48 seconds. Concordance between initial FS diagnosis and rendered through the MVD was 89%. Minor discrepancies made up 8% and major disagreements 3%. The kappa statistic for this series is 0.85. Participants rated the experience at 5 on a 10-point scale, range 3 to 7. Two-thirds found the image quality to be adequate, half were satisfied with image resolution, and 33% would be willing to make a diagnosis on the iPad, plus one only for special cases. Five of six respondents (83%) found the navigation with the study software difficult. Conclusion: Image fidelity and resolution makes the iPad potentially suitable for WSI evaluation of FS. Acceptable accuracy is attainable for FS interpretation. But, although possible to obtain acceptable results, use of the iPad with Interpath to view WSI is not easy and meets user resistance. The obstacle of slide navigation at high magnification could introduce frustrations, delays, or errors.
      Citation: Journal of Pathology Informatics 2011 2(1):41-41
      PubDate: Sat,27 Aug 2011
      DOI: 10.4103/2153-3539.84276
      Issue No: Vol. 2, No. 1 (2011)
       
  • Use of a laboratory information system driven tool for pre-signout quality
           assurance of random cytopathology reports
    • Authors: Sonal Kamat, Anil V Parwani, Walid E Khalbuss, Sara E Monaco, Susan M Kelly, Luke T Wiehagen, Anthony L Piccoli, Karen M Lassige, Liron Pantanowitz
      Pages: 42 - 42
      Abstract: Sonal Kamat, Anil V Parwani, Walid E Khalbuss, Sara E Monaco, Susan M Kelly, Luke T Wiehagen, Anthony L Piccoli, Karen M Lassige, Liron Pantanowitz

      Journal of Pathology Informatics 2011 2(1):42-42

      Background: Quality assurance (QA) programs in cytopathology laboratories in the USA currently primarily involve the review of Pap tests per clinical laboratory improvement amendments of 1988 federal regulations. A pre-signout quality assurance tool (PQAT) at our institution allows the laboratory information system (LIS) to also automatically and randomly select an adjustable percentage of non-gynecological cytopathology cases for review before release of the final report. The aim of this study was to review our experience and the effectiveness of this novel PQAT tool in cytology. Materials and Methods: Software modifications in the existing LIS application (CoPathPlus, Cerner) allow for the random QA of 8% of cases prior to signout. Selected cases are assigned to a second QA cytopathologist for review and all agreement and disagreements tracked. Detected errors are rectified before the case is signed out. Data from cases selected for PQAT over an 18-month period were collected and analyzed. Results: The total number of non-gynecological cases selected for QA review was 1339 (7.45%) out of 17,967 cases signed out during this time period. Most (1304) cases (97.4%) had an agreement in diagnosis. In 2.6% of cases, there were disagreements, including 34 minor and only 1 major disagreement. Average turnaround time of cases selected for review was not significantly altered. Conclusion: The PQAT provides a prospective QA mechanism in non-gynecological cytopathology to prevent diagnostic errors from occurring. This LIS-driven tool allows for peer review and corrective action to be taken prior to reporting without delaying turnaround time, thereby improving patient safety.
      Citation: Journal of Pathology Informatics 2011 2(1):42-42
      PubDate: Sat,27 Aug 2011
      DOI: 10.4103/2153-3539.84279
      Issue No: Vol. 2, No. 1 (2011)
       
  • Abstracts: Pathology Informatics 2011 Meeting
    • Pages: 43 - 43
      Abstract:

      Journal of Pathology Informatics 2011 2(1):43-43


      Citation: Journal of Pathology Informatics 2011 2(1):43-43
      PubDate: Tue,4 Oct 2011
      Issue No: Vol. 2, No. 1 (2011)
       
  • Autofocus methods of whole slide imaging systems and the introduction of a
           second-generation independent dual sensor scanning method
    • Authors: Michael C Montalto, Richard R McKay, Robert J Filkins
      Pages: 44 - 44
      Abstract: Michael C Montalto, Richard R McKay, Robert J Filkins

      Journal of Pathology Informatics 2011 2(1):44-44

      Accurate focusing is a critical challenge of whole slide imaging, primarily due to inherent tissue topography variability. Traditional line scanning and tile-based scanning systems are limited in their ability to acquire a high degree of focus points while still maintaining high throughput. This review examines limitations with first-generation whole slide scanning systems and explores a novel approach that employs continuous autofocus, referred to as independent dual sensor scanning. This "second-generation" concept decouples image acquisition from focusing, allowing for rapid scanning while maintaining continuous accurate focus. The technical concepts, merits, and limitations of this method are explained and compared to that of a traditional whole slide scanning system.
      Citation: Journal of Pathology Informatics 2011 2(1):44-44
      PubDate: Wed,19 Oct 2011
      DOI: 10.4103/2153-3539.86282
      Issue No: Vol. 2, No. 1 (2011)
       
  • High-definition hematoxylin and eosin staining in a transition to digital
           pathology
    • Authors: Jamie D Martina, Christopher Simmons, Drazen M Jukic
      Pages: 45 - 45
      Abstract: Jamie D Martina, Christopher Simmons, Drazen M Jukic

      Journal of Pathology Informatics 2011 2(1):45-45

      Introduction: A lot of attention has been generated in recent years by digital pathology and telepathology. Multiple reasons for and barriers to effective adoption are discussed in the current literature. Digital slides are the most promising medium at this time. The goal of our study was to evaluate whether the change in the methodology, particularly utilizing the so-called high-definition hematoxylin and eosin (H and E) slides, enhanced the quality of the final digital slide, and whether pathologists who tested the results perceived this as a difference in quality. Methods: The study was a blinded comparison of digital slides prepared using two methods: standard H&E batch staining and automated individual "high definition" HD HE staining. Four pathologists have compared 80 cases stained with each method. Results: The results discussed in this study show potential promise that the utilization of protocol(s) adapted for tissue and for imaging might be preferable for digital pathology in at least some of the pathology subspecialties. In particular, the protocol evaluated here was capable of turning out digital slides that had more contrast and detail, and therefore were perceived to provide enhanced diagnostically significant information for the pathologist.
      Citation: Journal of Pathology Informatics 2011 2(1):45-45
      PubDate: Wed,19 Oct 2011
      DOI: 10.4103/2153-3539.86284
      Issue No: Vol. 2, No. 1 (2011)
       
  • Evaluation and optimization for liquid-based preparation cytology in whole
           slide imaging
    • Authors: Roy E Lee, David S McClintock, Nora M Laver, Yukako Yagi
      Pages: 46 - 46
      Abstract: Roy E Lee, David S McClintock, Nora M Laver, Yukako Yagi

      Journal of Pathology Informatics 2011 2(1):46-46

      Background: Cytology poses different obstacles in whole slide imaging compared to surgical pathology slides. A single focal plane suffices for most of the latter, but cytology slides are thicker, potentially requiring multiple focal planes for adequate diagnostic information. Multiple focal planes adversely impact scanning time per slide, evaluation times, and file sizes. In this pilot study, we evaluated and compared the multilayer stack method to the extended focus algorithm as an alternative which collapses multiple focal planes into a single image, retaining only focused areas from each plane. Materials and Methods: 10 SurePath&#894; cervical cytology slides were scanned at three thickness settings: 18, 24, and 30 &#956;m. Three scanners were used: (1) Hamamatsu Nanozoomer 2.0-HT, (2) 3DHISTECH Mirax scan, and (3) Bioimagene iScan Coreo Au. The Nanozoomer and iScan utilized multilayer stacking, while the Mirax files were composited by extended focus. Scan times and file sizes were recorded, and image quality compared. Results: The Nanozoomer stacks averaged 1.58 gb and around 25 min for each slide, while the iScan stacks ranged from 6.23 to 9.3 gb and took 34-50 min to scan. The Mirax images averaged 210 mb and took 13-20 min to scan. Multilayer stack image quality from both Nanozoomer and iScan was fairly comparable. The iScan revealed significant mechanical issues that did not correspond to user settings. The Mirax images showed worrisome loss of crisp focus detail, worsening with increasing focal planes and impacting assessment of nuclear contours and chromatin detail. Conclusions: The optimal number of focal planes remains unknown for cytology. Multilayer stacks require excessive scanning time, network bandwidth, and file storage. Extended focus was evaluated as an alternative, but significant image quality issues were revealed. Further large-scale studies are needed to assess their clinical impact.
      Citation: Journal of Pathology Informatics 2011 2(1):46-46
      PubDate: Wed,19 Oct 2011
      DOI: 10.4103/2153-3539.86285
      Issue No: Vol. 2, No. 1 (2011)
       
  • Image microarrays (IMA): Digital pathology's missing tool
    • Authors: Jason Hipp, Jerome Cheng, Liron Pantanowitz, Stephen Hewitt, Yukako Yagi, James Monaco, Anant Madabhushi, Jaime Rodriguez-canales, Jeffrey Hanson, Sinchita Roy-Chowdhuri, Armando C Filie, Michael D Feldman, John E Tomaszewski, Natalie C Shih, Victor Brodsky, Giuseppe Giaccone, Michael R Emmert-Buck, Ulysses J Balis
      Pages: 47 - 47
      Abstract: Jason Hipp, Jerome Cheng, Liron Pantanowitz, Stephen Hewitt, Yukako Yagi, James Monaco, Anant Madabhushi, Jaime Rodriguez-canales, Jeffrey Hanson, Sinchita Roy-Chowdhuri, Armando C Filie, Michael D Feldman, John E Tomaszewski, Natalie C Shih, Victor Brodsky, Giuseppe Giaccone, Michael R Emmert-Buck, Ulysses J Balis

      Journal of Pathology Informatics 2011 2(1):47-47

      Introduction: The increasing availability of whole slide imaging (WSI) data sets (digital slides) from glass slides offers new opportunities for the development of computer-aided diagnostic (CAD) algorithms. With the all-digital pathology workflow that these data sets will enable in the near future, literally millions of digital slides will be generated and stored. Consequently, the field in general and pathologists, specifically, will need tools to help extract actionable information from this new and vast collective repository. Methods: To address this limitation, we designed and implemented a tool (dCORE) to enable the systematic capture of image tiles with constrained size and resolution that contain desired histopathologic features. Results: In this communication, we describe a user-friendly tool that will enable pathologists to mine digital slides archives to create image microarrays (IMAs). IMAs are to digital slides as tissue microarrays (TMAs) are to cell blocks. Thus, a single digital slide could be transformed into an array of hundreds to thousands of high quality digital images, with each containing key diagnostic morphologies and appropriate controls. Current manual digital image cut-and-paste methods that allow for the creation of a grid of images (such as an IMA) of matching resolutions are tedious. Conclusion: The ability to create IMAs representing hundreds to thousands of vetted morphologic features has numerous applications in education, proficiency testing, consensus case review, and research. Lastly, in a manner analogous to the way conventional TMA technology has significantly accelerated in situ studies of tissue specimens use of IMAs has similar potential to significantly accelerate CAD algorithm development.
      Citation: Journal of Pathology Informatics 2011 2(1):47-47
      PubDate: Sat,29 Oct 2011
      DOI: 10.4103/2153-3539.86829
      Issue No: Vol. 2, No. 1 (2011)
       
  • Standardization of whole slide image morphologic assessment with
           definition of a new application: Digital slide dynamic morphometry
    • Authors: Giacomo Puppa, Mauro Risio, Kieran Sheahan, Michael Vieth, Inti Zlobec, Alessandro Lugli, Sara Pecori, Lai Mun Wang, Cord Langner, Hiroyuki Mitomi, Takatoshi Nakamura, Masahiko Watanabe, Hideki Ueno, Jacques Chasle, Carlo Senore, Stephen A Conley, Paulette Herlin, Gregory Y Lauwers
      Pages: 48 - 48
      Abstract: Giacomo Puppa, Mauro Risio, Kieran Sheahan, Michael Vieth, Inti Zlobec, Alessandro Lugli, Sara Pecori, Lai Mun Wang, Cord Langner, Hiroyuki Mitomi, Takatoshi Nakamura, Masahiko Watanabe, Hideki Ueno, Jacques Chasle, Carlo Senore, Stephen A Conley, Paulette Herlin, Gregory Y Lauwers

      Journal of Pathology Informatics 2011 2(1):48-48

      Background: In histopathology, the quantitative assessment of various morphologic features is based on methods originally conceived on specific areas observed through the microscope used. Failure to reproduce the same reference field of view using a different microscope will change the score assessed. Visualization of a digital slide on a screen through a dedicated viewer allows selection of the magnification. However, the field of view is rectangular, unlike the circular field of optical microscopy. In addition, the size of the selected area is not evident, and must be calculated. Materials and Methods: A digital slide morphometric system was conceived to reproduce the various methods published for assessing tumor budding in colorectal cancer. Eighteen international experts in colorectal cancer were invited to participate in a web-based study by assessing tumor budding with five different methods in 100 digital slides. Results: The specific areas to be tested by each method were marked by colored circles. The areas were grouped in a target-like pattern and then saved as an .xml file. When a digital slide was opened, the .xml file was imported in order to perform the measurements. Since the morphometric tool is composed of layers that can be freely moved on top of the digital slide, the technique was named digital slide dynamic morphometry. Twelve investigators completed the task, the majority of them performing the multiple evaluations of each of the cases in less than 12 minutes. Conclusions: Digital slide dynamic morphometry has various potential applications and might be a useful tool for the assessment of histologic parameters originally conceived for optical microscopy that need to be quantified.
      Citation: Journal of Pathology Informatics 2011 2(1):48-48
      PubDate: Sat,29 Oct 2011
      DOI: 10.4103/2153-3539.86830
      Issue No: Vol. 2, No. 1 (2011)
       
  • Review of methods in medical informatics: Fundamentals of healthcare
           programming in Perl, Python and Ruby by Jules J. Berman
    • Authors: Alexis B Carter
      Pages: 49 - 49
      Abstract: Alexis B Carter

      Journal of Pathology Informatics 2011 2(1):49-49


      Citation: Journal of Pathology Informatics 2011 2(1):49-49
      PubDate: Sat,29 Oct 2011
      Issue No: Vol. 2, No. 1 (2011)
       
  • High-throughput profiling of tissue and tissue model microarrays: Combined
           transmitted light and 3-color fluorescence digital pathology
    • Authors: Michel Nederlof, Shigeo Watanabe, Bill Burnip, D Lansing Taylor, Rebecca Critchley-Thorne
      Pages: 50 - 50
      Abstract: Michel Nederlof, Shigeo Watanabe, Bill Burnip, D Lansing Taylor, Rebecca Critchley-Thorne

      Journal of Pathology Informatics 2011 2(1):50-50

      For many years pathologists have used Hematoxylin and Eosin (H&E), single marker immunohistochemistry (IHC) and in situ hybridization with manual analysis by microscopy or at best simple digital imaging. There is a growing trend to update pathology to a digital workflow to improve objectivity and productivity, as has been done in radiology. There is also a need for tissue-based multivariate biomarker assays to improve the accuracy of diagnostic, prognostic, and predictive testing. Multivariate tests are not compatible with the traditional single marker, manual analysis pathology methods but instead require a digital platform with brightfield and fluorescence imaging, quantitative image analysis, and informatics. Here we describe the use of the Hamamatsu NanoZoomer Digital Pathology slide scanner with HCImage software for combined brightfield and multiplexed fluorescence biomarker analysis and highlight its applications in biomarker research and pathology testing. This combined approach will be an important aid to pathologists in making critical diagnoses.
      Citation: Journal of Pathology Informatics 2011 2(1):50-50
      PubDate: Tue,15 Nov 2011
      DOI: 10.4103/2153-3539.89849
      Issue No: Vol. 2, No. 1 (2011)
       
  • Telecytology: Clinical applications, current challenges, and future
           benefits
    • Authors: Michael Thrall, Liron Pantanowitz, Walid Khalbuss
      Pages: 51 - 51
      Abstract: Michael Thrall, Liron Pantanowitz, Walid Khalbuss

      Journal of Pathology Informatics 2011 2(1):51-51

      Telecytology is the interpretation of cytology material at a distance using digital images. For more than a decade, pioneering efforts to introduce telecytology into clinical practice have been reported. A Medline search for "telecytology" and "cytology" reveals a voluminous literature, though much of what has been published to date is based on technologies that are rapidly becoming obsolete. The technological limitations of previous techniques, including the transmission of static digital images and dynamic streaming images, have limited telecytology to minor niches. The primary problem with these technologies is that the remote viewer can only see a small fraction of the material on the original slides, introducing the possibility of diagnostic error based not only on image quality but also on image selection. Remote robotic microscopy offers one possible solution to this problem, but to date has found limited acceptance, principally attributable to slow operating times. Whole slide imaging seems to be a much more promising solution, though cytology-specific literature regarding its use is still scant. The advent of whole slide imaging opens up new possibilities for telecytology by enabling high-quality images of entire cytology specimens to be available to anyone, anywhere via the Internet. Although challenges remain, especially with regard to capturing the full microscopy experience including multiple planes of focus and sharp high-powered images, rapidly advancing technology promises to overcome these limitations. Increasing application of whole slide imaging technology in surgical pathology will undoubtedly also increase its application to cytology due to the increasing affordability and practicality of the equipment as it serves a larger number of useful roles within a pathology department. The current and expanding applications of telecytology for clinical practice, education, quality assurance, and testing will be reviewed.
      Citation: Journal of Pathology Informatics 2011 2(1):51-51
      PubDate: Mon,26 Dec 2011
      DOI: 10.4103/2153-3539.91129
      Issue No: Vol. 2, No. 1 (2011)
       
  • An open-source software program for performing Bonferroni and related
           corrections for multiple comparisons
    • Authors: Kyle Lesack, Christopher Naugler
      Pages: 52 - 52
      Abstract: Kyle Lesack, Christopher Naugler

      Journal of Pathology Informatics 2011 2(1):52-52

      Increased type I error resulting from multiple statistical comparisons remains a common problem in the scientific literature. This may result in the reporting and promulgation of spurious findings. One approach to this problem is to correct groups of P-values for "family-wide significance" using a Bonferroni correction or the less conservative Bonferroni-Holm correction or to correct for the "false discovery rate" with a Benjamini-Hochberg correction. Although several solutions are available for performing this correction through commercially available software there are no widely available easy to use open source programs to perform these calculations. In this paper we present an open source program written in Python 3.2 that performs calculations for standard Bonferroni, Bonferroni-Holm and Benjamini-Hochberg corrections.
      Citation: Journal of Pathology Informatics 2011 2(1):52-52
      PubDate: Mon,26 Dec 2011
      DOI: 10.4103/2153-3539.91130
      Issue No: Vol. 2, No. 1 (2011)
       
  • Heterogeneity of publicly accessible online critical values for
           therapeutic drugs
    • Authors: Colt M McClain, Richard Owings, Joshua A Bornhorst
      Pages: 53 - 53
      Abstract: Colt M McClain, Richard Owings, Joshua A Bornhorst

      Journal of Pathology Informatics 2011 2(1):53-53

      Introduction: Critical values are reported to clinicians when laboratory values are life threatening and require immediate attention. To date no definitive critical value limit recommendations have been produced regarding therapeutic drug monitoring. Some laboratories choose to publish critical value lists online. These publicly available values may be accessed and potentially utilized by laboratory staff, patient care providers, and patients. Materials and Methods: A web-based search of laboratories associated with the Accreditation Council for Graduate Medical Education pathology residency programs was initiated to determine which therapeutic drugs had critical values and to examine the degree of variation in published critical values for these institutions. Results: Of the 107 institutions with university-based pathology training programs, 36 had published critical values online for review. Thirteen therapeutic drugs were investigated and the number of institutions reporting critical value limits for the drug, as well as the median, range, standard deviation, and the coefficient of variation of critical value concentration limits for each drug were determined. A number of the online critical value limits were deemed to be erroneous, most likely due to incorrectly listed units of measurement. Conclusions: There was a large degree of heterogeneity with regard to the chosen critical value limits for therapeutic drugs. This wide variance in critical values appears to be greater than that observed in interassay proficiency testing. Institutions should reexamine the rationale for their current critical value parameters and ensure that critical value limits and associated units are accurately published online.
      Citation: Journal of Pathology Informatics 2011 2(1):53-53
      PubDate: Mon,26 Dec 2011
      DOI: 10.4103/2153-3539.91131
      Issue No: Vol. 2, No. 1 (2011)
       
  • Introducing the Journal of Pathology Informatics
    • Authors: Liron Pantanowitz, Anil V Parwani
      Pages: 1 - 1
      Abstract: Liron Pantanowitz, Anil V Parwani

      Journal of Pathology Informatics 2010 1(1):1-1


      Citation: Journal of Pathology Informatics 2010 1(1):1-1
      PubDate: Wed,26 May 2010
      DOI: 10.4103/2153-3539.63821
      Issue No: Vol. 1, No. 1 (2010)
       
  • Development and use of a genitourinary pathology digital teaching set for
           trainee education
    • Authors: Li Li, Bryan J Dangott, Anil V Parwani
      Pages: 2 - 2
      Abstract: Li Li, Bryan J Dangott, Anil V Parwani

      Journal of Pathology Informatics 2010 1(1):2-2

      Background : Automated, high-speed, high-resolution whole slide imaging (WSI) robots are becoming increasingly robust and capable. This technology has started to have a significant impact on pathology practice in various aspects including resident education. To be sufficient and adequate, training in pathology requires gaining broad exposure to various diagnostic patterns through teaching sets, which are traditionally composed of glass slides. Methods: A teaching set of over 295 glass slides has been used for resident training at the Division of Genitourinary Pathology, Department of Pathology, University of Pittsburgh Medical Center. Whole slide images were prepared from these slides using an Aperio ScanScope CS scanner. These images and case-related information were uploaded on a web-based digital teaching model. Results: The web site is available at: https://www.secure.opi.upmc.edu/genitourinary/index.cfm. Once logged in, users can view the list of cases, or search cases with or without diagnoses shown. Each case can be accessed through an option button, where the clinical history, gross findings are initially shown. Whole slide images can be accessed through the links on the page, which allows users to make diagnoses on their own. More information including final diagnosis will display when the diagnosis-button is clicked. Conclusion: The web-based digital study set provides additional educational benefits to using glass slides. Residents or other users can remotely access whole slide images and related information at their convenience. Searching and sorting functions and self-testing mode allow a more targeted study. It would also prepare residents with competence to work with whole slide images. Further, the model can be expanded to include pre-rotation and post-rotation exams, and/or a virtual rotation system, which may potentially make standardization of pathology resident training possible in the future.
      Citation: Journal of Pathology Informatics 2010 1(1):2-2
      PubDate: Wed,26 May 2010
      DOI: 10.4103/2153-3539.63822
      Issue No: Vol. 1, No. 1 (2010)
       
  • Overview of laboratory data tools available in a single electronic medical
           record
    • Authors: Neil R Kudler, Liron Pantanowitz
      Pages: 3 - 3
      Abstract: Neil R Kudler, Liron Pantanowitz

      Journal of Pathology Informatics 2010 1(1):3-3

      Background: Laboratory data account for the bulk of data stored in any given electronic medical record (EMR). To best serve the user, electronic laboratory data needs to be flexible and customizable. Our aim was to determine the various ways in which laboratory data get utilized by clinicians in our health system's EMR. Method: All electronic menus, tabs, flowsheets, notes and subsections within the EMR (Millennium v2007.13, Cerner Corporation, Kansas City, MO, US) were explored to determine how clinicians utilize discrete laboratory data. Results: Laboratory data in the EMR were utilized by clinicians in five distinct ways: within flowsheets, their personal inbox (EMR messaging), with decision support tools, in the health maintenance tool, and when incorporating laboratory data into their clinical notes and letters. Conclusions : Flexible electronic laboratory data in the EMR hava many advantages. Users can view, sort, pool, and appropriately route laboratory information to better support trend analyses, clinical decision making, and clinical charting. Laboratory data in the EMR can also be utilized to develop clinical decision support tools. Pathologists need to participate in the creation of these EMR tools in order to better support the appropriate utilization of laboratory information in the EMR.
      Citation: Journal of Pathology Informatics 2010 1(1):3-3
      PubDate: Wed,26 May 2010
      DOI: 10.4103/2153-3539.63824
      Issue No: Vol. 1, No. 1 (2010)
       
  • Cytologic evaluation of image-guided fine needle aspiration biopsies via
           robotic microscopy: A validation study
    • Authors: Guoping Cai, Lisa A Teot, Walid E Khalbuss, Jing Yu, Sara E Monaco, Drazen M Jukic, Anil V Parwani
      Pages: 4 - 4
      Abstract: Guoping Cai, Lisa A Teot, Walid E Khalbuss, Jing Yu, Sara E Monaco, Drazen M Jukic, Anil V Parwani

      Journal of Pathology Informatics 2010 1(1):4-4

      Background: This study carried out was to assess the feasibility of using robotic microscopy (RM) for cytologic evaluation of direct smears from fine needle aspiration biopsy (FNAB). Methods: Three board-certified cytopathologists reviewed representative direct smears from 40 image-guided FNABs using RM and subsequently re-reviewed the same smears using conventional microscopy. Adequacy of the smears and cytologic diagnosis, as determined using the two approaches, were compared for each individual cytopathologist (intraobserver) and between the three cytopathologists (interobserver). The intraobserver and interobserver discrepancies were analyzed and discussed in a follow-up consensus conference. Results: For assessment of adequacy, there were high concordance rates (intraobserver: 92.5-97.5%; interobserver: 90-92.5%), with a few discrepancies involving distinctions between suboptimal and satisfactory smears. Analysis of diagnostic interpretations showed correct classification of 92.5-95% (intraobserver) or 90-92.5% (interobserver) of benign and malignant cases combined, with the discrepancies being between benign and atypical cells in the benign group, and between suspicious and malignant in the malignant group. Within the malignant group, 94% of cases were accurately subclassified via RM. The quality of images viewed by using RM was rated adequate (fair or good) for 95% of the slides. Conclusions: The results demonstrate that cytologic evaluation of direct smears from FNABs using RM is feasible. Problems encountered included the longer times needed to evaluate cases with thick, bloody smears and/or low numbers of diagnostic cells, and difficulties in recognizing neuroendocrine differentiation and mimics of hepatocellular carcinoma.
      Citation: Journal of Pathology Informatics 2010 1(1):4-4
      PubDate: Wed,26 May 2010
      DOI: 10.4103/2153-3539.63826
      Issue No: Vol. 1, No. 1 (2010)
       
  • Stepwise approach to establishing multiple outreach laboratory information
           system-electronic medical record interfaces
    • Authors: Liron Pantanowitz, Wayne LaBranche, William Lareau
      Pages: 5 - 5
      Abstract: Liron Pantanowitz, Wayne LaBranche, William Lareau

      Journal of Pathology Informatics 2010 1(1):5-5

      Clinical laboratory outreach business is changing as more physician practices adopt an electronic medical record (EMR). Physician connectivity with the laboratory information system (LIS) is consequently becoming more important. However, there are no reports available to assist the informatician with establishing and maintaining outreach LIS-EMR connectivity. A four-stage scheme is presented that was successfully employed to establish unidirectional and bidirectional interfaces with multiple physician EMRs. This approach involves planning (step 1), followed by interface building (step 2) with subsequent testing (step 3), and finally ongoing maintenance (step 4). The role of organized project management, software as a service (SAAS), and alternate solutions for outreach connectivity are discussed.
      Citation: Journal of Pathology Informatics 2010 1(1):5-5
      PubDate: Wed,26 May 2010
      DOI: 10.4103/2153-3539.63829
      Issue No: Vol. 1, No. 1 (2010)
       
  • HIMSS10 - Perspectives from a newcomer pathologist and a seasoned attendee
           pathologist: Pathologists should attend!
    • Authors: Alexis B Carter, Raymond Aller
      Pages: 6 - 6
      Abstract: Alexis B Carter, Raymond Aller

      Journal of Pathology Informatics 2010 1(1):6-6


      Citation: Journal of Pathology Informatics 2010 1(1):6-6
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65340
      Issue No: Vol. 1, No. 1 (2010)
       
  • Whole slide imaging for teleconsultation and clinical use
    • Authors: Bryan Dangott, Anil Parwani
      Pages: 7 - 7
      Abstract: Bryan Dangott, Anil Parwani

      Journal of Pathology Informatics 2010 1(1):7-7


      Citation: Journal of Pathology Informatics 2010 1(1):7-7
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65342
      Issue No: Vol. 1, No. 1 (2010)
       
  • Development of electronic medical record charting for hospital-based
           transfusion and apheresis medicine services: Early adoption perspectives
    • Authors: Rebecca Levy, Liron Pantanowitz, Darlene Cloutier, Jean Provencher, Joan McGirr, Jennifer Stebbins, Suzanne Cronin, Josh Wherry, Joseph Fenton, Eileen Donelan, Vandita Johari, Chester Andrzejewski
      Pages: 8 - 8
      Abstract: Rebecca Levy, Liron Pantanowitz, Darlene Cloutier, Jean Provencher, Joan McGirr, Jennifer Stebbins, Suzanne Cronin, Josh Wherry, Joseph Fenton, Eileen Donelan, Vandita Johari, Chester Andrzejewski

      Journal of Pathology Informatics 2010 1(1):8-8

      Background: Electronic medical records (EMRs) provide universal access to health care information across multidisciplinary lines. In pathology departments, transfusion and apheresis medicine services (TAMS) involved in direct patient care activities produce data and documentation that typically do not enter the EMR. Taking advantage of our institution's initiative for implementation of a paperless medical record, our TAMS division set out to develop an electronic charting (e-charting) strategy within the EMR. Methods: A focus group of our hospital's transfusion committee consisting of transfusion medicine specialists, pathologists, residents, nurses, hemapheresis specialists, and information technologists was constituted and charged with the project. The group met periodically to implement e-charting TAMS workflow and produced electronic documents within the EMR (Cerner Millenium) for various service line functions. Results: The interdisciplinary working group developed and implemented electronic versions of various paper-based clinical documentation used by these services. All electronic notes collectively gather and reside within a unique Transfusion Medicine Folder tab in the EMR, available to staff with access to patient charts. E-charting eliminated illegible handwritten notes, resulted in more consistent clinical documentation among staff, and provided greater real-time review/access of hemotherapy practices. No major impediments to workflow or inefficiencies have been encountered. However, minor updates and corrections to documents as well as select work re-designs were required for optimal use of e-charting by these services. Conclusion: Documentation of pathology subspecialty activities such as TAMS can be successfully incorporated into the EMR. E-charting by staff enhances communication and helps promote standardized documentation of patient care within and across service lines. Well-constructed electronic documents in the EMR may also enhance data mining, quality improvement, and biovigilance monitoring activities.
      Citation: Journal of Pathology Informatics 2010 1(1):8-8
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65345
      Issue No: Vol. 1, No. 1 (2010)
       
  • The tissue microarray OWL schema: An open-source tool for sharing tissue
           microarray data
    • Authors: Hyunseok P Kang, Charles D Borromeo, Jules J Berman, Michael J Becich
      Pages: 9 - 9
      Abstract: Hyunseok P Kang, Charles D Borromeo, Jules J Berman, Michael J Becich

      Journal of Pathology Informatics 2010 1(1):9-9

      Background: Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.
      Citation: Journal of Pathology Informatics 2010 1(1):9-9
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65347
      Issue No: Vol. 1, No. 1 (2010)
       
  • The pathology informatics curriculum wiki: Harnessing the power of
           user-generated content
    • Authors: Ji Yeon Kim, Thomas M Gudewicz, Anand S Dighe, John R Gilbertson
      Pages: 10 - 10
      Abstract: Ji Yeon Kim, Thomas M Gudewicz, Anand S Dighe, John R Gilbertson

      Journal of Pathology Informatics 2010 1(1):10-10

      Background: The need for informatics training as part of pathology training has never been so critical, but pathology informatics is a wide and complex field and very few programs currently have the resources to provide comprehensive educational pathology informatics experiences to their residents. In this article, we present the "pathology informatics curriculum wiki", an open, on-line wiki that indexes the pathology informatics content in a larger public wiki, Wikipedia, (and other online content) and organizes it into educational modules based on the 2003 standard curriculum approved by the Association for Pathology Informatics (API). Methods and Results: In addition to implementing the curriculum wiki at http://pathinformatics.wikispaces.com, we have evaluated pathology informatics content in Wikipedia. Of the 199 non-duplicate terms in the API curriculum, 90% have at least one associated Wikipedia article. Furthermore, evaluation of articles on a five-point Likert scale showed high scores for comprehensiveness (4.05), quality (4.08), currency (4.18), and utility for the beginner (3.85) and advanced (3.93) learners. These results are compelling and support the thesis that Wikipedia articles can be used as the foundation for a basic curriculum in pathology informatics. Conclusions: The pathology informatics community now has the infrastructure needed to collaboratively and openly create, maintain and distribute the pathology informatics content worldwide (Wikipedia) and also the environment (the curriculum wiki) to draw upon its own resources to index and organize this content as a sustainable basic pathology informatics educational resource. The remaining challenges are numerous, but largest by far will be to convince the pathologists to take the time and effort required to build pathology informatics content in Wikipedia and to index and organize this content for education in the curriculum wiki.
      Citation: Journal of Pathology Informatics 2010 1(1):10-10
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65428
      Issue No: Vol. 1, No. 1 (2010)
       
  • Computerized provider order entry systems - Research imperatives and
           organizational challenges facing pathology services
    • Authors: Andrew Georgiou, Johanna Westbrook, Jeffrey Braithwaite
      Pages: 11 - 11
      Abstract: Andrew Georgiou, Johanna Westbrook, Jeffrey Braithwaite

      Journal of Pathology Informatics 2010 1(1):11-11

      Information and communication technologies (ICT) are contributing to major changes taking place in pathology and within health services more generally. In this article, we draw on our research experience for over 7 years investigating the implementation and diffusion of computerized provider order entry (CPOE) systems to articulate some of the key informatics challenges confronting pathology laboratories. The implementation of these systems, with their improved information management and decision support structures, provides the potential for enhancing the role that pathology services play in patient care pathways. Beyond eliminating legibility problems, CPOE systems can also contribute to the efficiency and safety of healthcare, reducing the duplication of test orders and diminishing the risk of misidentification of patient samples and orders. However, despite the enthusiasm for CPOE systems, their diffusion across healthcare settings remains variable and is often beset by implementation problems. Information systems like CPOE may have the ability to integrate work, departments and organizations, but unfortunately, health professionals, departments and organizations do not always want to be integrated in ways that information systems allow. A persistent theme that emerges from the research evidence is that one size does not fit all, and system success or otherwise is reliant on the conditions and circumstances in which they are located. These conditions and circumstances are part of what is negotiated in the complex, messy and challenging area of ICT implementation. The solution is not likely to be simple and easy, but current evidence suggests that a combination of concerted efforts, better research designs, more sophisticated theories and hypotheses as well as more skilled, multidisciplinary research teams, tackling this area of study will bring substantial benefits, improving the effectiveness of pathology services, and, as a direct corollary, the quality of patient care.
      Citation: Journal of Pathology Informatics 2010 1(1):11-11
      PubDate: Tue,13 Jul 2010
      DOI: 10.4103/2153-3539.65431
      Issue No: Vol. 1, No. 1 (2010)
       
  • A decade of experience in the development and implementation of tissue
           banking informatics tools for intra and inter-institutional translational
           research
    • Authors: Waqas Amin, Harpreet Singh, Andre K Pople, Sharon Winters, Rajiv Dhir, Anil V Parwani, Michael J Becich
      Pages: 12 - 12
      Abstract: Waqas Amin, Harpreet Singh, Andre K Pople, Sharon Winters, Rajiv Dhir, Anil V Parwani, Michael J Becich

      Journal of Pathology Informatics 2010 1(1):12-12

      Context: Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models. Design: Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 9.2.0.1 server tools and software applications and the model-driven architecture is implemented in a J2EE framework. Result: The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource ( http://www.cpctr.info/ ), Pennsylvania Cancer Alliance Bioinformatics Consortium ( http://pcabc.upmc.edu/main.cfm ), EDRN Colorectal and Pancreatic Neoplasm Database ( http://edrn.nci.nih.gov/ ) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database ( http://spores.nci.nih.gov/current/hn/index.htm ). The model-based architecture is represented by the National Mesothelioma Virtual Bank ( http://mesotissue.org/ ). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet. Conclusion: These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems.
      Citation: Journal of Pathology Informatics 2010 1(1):12-12
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68314
      Issue No: Vol. 1, No. 1 (2010)
       
  • The state of telepathology in Japan
    • Authors: Takashi Sawai, Miwa Uzuki, Akihisa Kamataki, Ikuo Tofukuji
      Pages: 13 - 13
      Abstract: Takashi Sawai, Miwa Uzuki, Akihisa Kamataki, Ikuo Tofukuji

      Journal of Pathology Informatics 2010 1(1):13-13

      Telepathology began in Japan in the early 1990s in response to advances in computing and telecommunications equipment development and a dearth of pathologists. Telepathology in Japan is most often used for rapid intraoperative pathological diagnosis using frozen section, followed by second opinions and consultation. Intraoperatively, telepathology is used to determine malignancy, metastasis of malignant tumors, and the extent of excision. Infrastructure and equipment has evolved from analog lines to digital lines like integrated services digital network (ISDN) and asymmetric digital subscriber line (ADSL), and recently to fiber optics. The use of communications satellites is also being considered. Image quality is being improved to Hi-Vision (HDTV), and from still images to real-time video. Digital microscopy has been introduced, and is used in education and consultation.
      Citation: Journal of Pathology Informatics 2010 1(1):13-13
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68327
      Issue No: Vol. 1, No. 1 (2010)
       
  • Medical education in the digital age: Digital whole slide imaging as an
           e-learning tool
    • Authors: Kirk Foster
      Pages: 14 - 14
      Abstract: Kirk Foster

      Journal of Pathology Informatics 2010 1(1):14-14


      Citation: Journal of Pathology Informatics 2010 1(1):14-14
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68331
      Issue No: Vol. 1, No. 1 (2010)
       
  • Digital images and the future of digital pathology
    • Authors: Liron Pantanowitz
      Pages: 15 - 15
      Abstract: Liron Pantanowitz

      Journal of Pathology Informatics 2010 1(1):15-15


      Citation: Journal of Pathology Informatics 2010 1(1):15-15
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68332
      Issue No: Vol. 1, No. 1 (2010)
       
  • Application of virtual microscopy in consultation practice of
           gastrointestinal and liver pathology
    • Authors: Shriram Jakate
      Pages: 16 - 16
      Abstract: Shriram Jakate

      Journal of Pathology Informatics 2010 1(1):16-16


      Citation: Journal of Pathology Informatics 2010 1(1):16-16
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68333
      Issue No: Vol. 1, No. 1 (2010)
       
  • Digital pathology in clinical consultation practice
    • Authors: Subodh M Lele
      Pages: 17 - 17
      Abstract: Subodh M Lele

      Journal of Pathology Informatics 2010 1(1):17-17


      Citation: Journal of Pathology Informatics 2010 1(1):17-17
      PubDate: Tue,10 Aug 2010
      DOI: 10.4103/2153-3539.68334
      Issue No: Vol. 1, No. 1 (2010)
       
  • Abstracts: Pathology Informatics 2010 Meeting
    • Pages: 18 - 18
      Abstract:

      Journal of Pathology Informatics 2010 1(1):18-18


      Citation: Journal of Pathology Informatics 2010 1(1):18-18
      PubDate: Sat,18 Sep 2010
      Issue No: Vol. 1, No. 1 (2010)
       
  • Optimizing the pathology workstation "cockpit": Challenges and
           solutions
    • Authors: Elizabeth A Krupinski
      Pages: 19 - 19
      Abstract: Elizabeth A Krupinski

      Journal of Pathology Informatics 2010 1(1):19-19

      The 21 st century has brought numerous changes to the clinical reading (i.e., image or virtual pathology slide interpretation) environment of pathologists and it will continue to change even more dramatically as information and communication technologies (ICTs) become more widespread in the integrated healthcare enterprise. The extent to which these changes impact the practicing pathologist differ as a function of the technology under consideration, but digital "virtual slides" and the viewing of images on computer monitors instead of glass slides through a microscope clearly represents a significant change in the way that pathologists extract information from these images and render diagnostic decisions. One of the major challenges facing pathologists in this new era is how to best optimize the pathology workstation, the reading environment and the new and varied types of information available in order to ensure efficient and accurate processing of this information. Although workstations can be stand-alone units with images imported via external storage devices, this scenario is becoming less common as pathology departments connect to information highways within their hospitals and to external sites. Picture Archiving and Communications systems are no longer confined to radiology departments but are serving the entire integrated healthcare enterprise, including pathology. In radiology, the workstation is often referred to as the "cockpit" with a "digital dashboard" and the reading room as the "control room." Although pathology has yet to "go digital" to the extent that radiology has, lessons derived from radiology reading "cockpits" can be quite valuable in setting up the digital pathology reading room. In this article, we describe the concept of the digital dashboard and provide some recent examples of informatics-based applications that have been shown to improve the workflow and quality in digital reading environments.
      Citation: Journal of Pathology Informatics 2010 1(1):19-19
      PubDate: Fri,1 Oct 2010
      DOI: 10.4103/2153-3539.70708
      Issue No: Vol. 1, No. 1 (2010)
       
  • Ten important lessons we have learned as pathology bloggers
    • Authors: Keith J Kaplan, Bruce A Friedman, Mark D Pool
      Pages: 20 - 20
      Abstract: Keith J Kaplan, Bruce A Friedman, Mark D Pool

      Journal of Pathology Informatics 2010 1(1):20-20


      Citation: Journal of Pathology Informatics 2010 1(1):20-20
      PubDate: Fri,1 Oct 2010
      DOI: 10.4103/2153-3539.70709
      Issue No: Vol. 1, No. 1 (2010)
       
  • Tolerance testing of passive radio frequency identification tags for
           solvent, temperature, and pressure conditions encountered in an anatomic
           pathology or biorepository setting
    • Authors: Alina A Leung, Jerry J Lou, Sergey Mareninov, Steven S Silver, Mark J Routbort, Michael Riben, Gary Andrechak, William H Yong
      Pages: 21 - 21
      Abstract: Alina A Leung, Jerry J Lou, Sergey Mareninov, Steven S Silver, Mark J Routbort, Michael Riben, Gary Andrechak, William H Yong

      Journal of Pathology Informatics 2010 1(1):21-21

      Background: Radio frequency identification (RFID) tags have potential for use in identifying and tracking biospecimens in anatomic pathology and biorepository laboratories. However, there is little to no data on the tolerance of tags to solutions, solvents, temperatures, and pressures likely to be encountered in the laboratory. The functioning of the Hitachi Mu-chip RFID tag, a candidate for pathology use, was evaluated under such conditions. Methods: The RFID tags were affixed to cryovials containing tissue or media, glass slides, and tissue cassettes. The tags were interrogated for readability before and after each testing condition or cycle. Individual tags were subjected to only one testing condition but for multiple cycles. Testing conditions were: 1) Ten wet autoclave cycles (121&#730;C, 15 psi); 2) Ten dry autoclave cycles (121&#730;C, 26 psi); 3) Ten tissue processor cycles; 4) Ten hematoxylin and eosin (H&E) staining cycles; 5) Ten antigen retrieval pressure cooker cycles (125&#730;C, 15 psi); 6) 75 o C for seven days; 7) 75-59 o C day/night cycles for 7 days; 8) -80 o C, -150 o C, or -196 o C for 12 months; 9) Fifty freeze-thaw cycles (-196 o C to 22 o C). Results: One hundred percent of tags exposed to cold temperatures from -80 to -196 o C (80 tags, 1120 successful reads), high temperatures from 52 to 75 o C (40 tags, 420 reads), H & E staining (20 tags, 200 reads), pressure cooker antigen retrieval (20 tags, 200 reads), and wet autoclaving (20 tags, 200 reads) functioned well throughout and after testing. Of note, all 20 tested tags tolerated 50 freeze-thaw cycles and all 60 tags subjected to sustained freezing temperatures were readable after 1 year. One dry autoclaved tag survived nine cycles but failed after the tenth. The remaining 19 tags were readable after all 10 dry autoclave cycles. One tag failed after the first tissue processing cycle while the remaining 19 tags survived all 10 tissue processing cycles. Conclusions: In this preliminary study, these RFID tags show a high-degree of tolerance to tested solutions, solvents, temperature, and pressure conditions. However, a measurable failure rate is detectable under some circumstances and redundant identification systems such as barcodes may be required with the deployment of RFID systems. We have delineated testing protocols that may be used as a framework for preliminary assessments of candidate RFID tag tolerance to laboratory conditions.
      Citation: Journal of Pathology Informatics 2010 1(1):21-21
      PubDate: Fri,1 Oct 2010
      DOI: 10.4103/2153-3539.70710
      Issue No: Vol. 1, No. 1 (2010)
       
  • Design and utilization of the colorectal and pancreatic neoplasm virtual
           biorepository: An early detection research network initiative
    • Authors: Waqas Amin, Harpreet Singh, Lynda Ann Dzubinski, Robert E Schoen, Anil V Parwani
      Pages: 22 - 22
      Abstract: Waqas Amin, Harpreet Singh, Lynda Ann Dzubinski, Robert E Schoen, Anil V Parwani

      Journal of Pathology Informatics 2010 1(1):22-22

      Background: The Early Detection Research Network (EDRN) colorectal and pancreatic neoplasm virtual biorepository is a bioinformatics-driven system that provides high-quality clinicopathology-rich information for clinical biospecimens. This NCI-sponsored EDRN resource supports translational cancer research. The information model of this biorepository is based on three components: (a) development of common data elements (CDE), (b) a robust data entry tool and (c) comprehensive data query tools. Methods: The aim of the EDRN initiative is to develop and sustain a virtual biorepository for support of translational research. High-quality biospecimens were accrued and annotated with pertinent clinical, epidemiologic, molecular and genomic information. A user-friendly annotation tool and query tool was developed for this purpose. The various components of this annotation tool include: CDEs are developed from the College of American Pathologists (CAP) Cancer Checklists and North American Association of Central Cancer Registries (NAACR) standards. The CDEs provides semantic and syntactic interoperability of the data sets by describing them in the form of metadata or data descriptor. The data entry tool is a portable and flexible Oracle-based data entry application, which is an easily mastered, web-based tool. The data query tool facilitates investigators to search deidentified information within the warehouse through a "point and click" interface thus enabling only the selected data elements to be essentially copied into a data mart using a dimensional-modeled structure from the warehouse's relational structure. Results: The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository database contains multimodal datasets that are available to investigators via a web-based query tool. At present, the database holds 2,405 cases and 2,068 tumor accessions. The data disclosure is strictly regulated by user's authorization. The high-quality and well-characterized biospecimens have been used in different translational science research projects as well as to further various epidemiologic and genomics studies. Conclusions: The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository with a tangible translational biomedical informatics infrastructure facilitates translational research. The data query tool acts as a central source and provides a mechanism for researchers to efficiently query clinically annotated datasets and biospecimens that are pertinent to their research areas. The tool ensures patient health information protection by disclosing only deidentified data with Institutional Review Board and Health Insurance Portability and Accountability Act protocols.
      Citation: Journal of Pathology Informatics 2010 1(1):22-22
      PubDate: Fri,1 Oct 2010
      DOI: 10.4103/2153-3539.70831
      Issue No: Vol. 1, No. 1 (2010)
       
  • The use of multispectral imaging to distinguish reactive urothelium from
           neoplastic urothelium
    • Authors: Christopher Michael Gilbert, Anil Parwani
      Pages: 23 - 23
      Abstract: Christopher Michael Gilbert, Anil Parwani

      Journal of Pathology Informatics 2010 1(1):23-23

      Context: The interpretation of urothelial atypia in a setting of chronic inflammation and reactive changes can prove difficult with small biopsies. Limited recuts lessen the efficacy of ancillary studies such as CK20, P53 and CD44 in these instances. Objective: To evaluate a triple-immunostain with the assistance of multispectral microscopy. Design: Fifty-three bladder biopsies with previous diagnosis of benign/reactive, dysplastic, carcinoma in situ or carcinoma were prepared using a triple-immunostain cocktail consisting of CK20, P53 and CD44. Three control stains were used for the purpose of creating a spectral library for the Nuance CRI Flex microscopy system. All specimens were interpreted by light microscopy, processed with the Nuance 2.71 software, and CK20 and P53 were scored blinded to the case diagnoses. CD44 was not scored as it proved difficult to interpret in many cases. Results: The results demonstrated that it was possible to separate CK20, P53 and the counterstain that were co-localized in the biopsies. Separation of the stains demonstrated a correlation of p53 and CK20 dual expression in biopsies diagnosed as carcinoma. Low or undetectable levels of expression were seen in biopsies later diagnosed as reactive or benign. Conclusion: The combination of multispectral microscopy and multiple immunostain cocktails form a powerful and useful tool for the interpretation of small biopsies with faint or difficult to interpret staining and for cases with limited material such as small-bladder biopsies.
      Citation: Journal of Pathology Informatics 2010 1(1):23-23
      PubDate: Mon,11 Oct 2010
      DOI: 10.4103/2153-3539.71064
      Issue No: Vol. 1, No. 1 (2010)
       
  • Automated ancillary cancer history classification for mesothelioma
           patients from free-text clinical reports
    • Authors: Richard A Wilson, Wendy W Chapman, Shawn J DeFries, Michael J Becich, Brian E Chapman
      Pages: 24 - 24
      Abstract: Richard A Wilson, Wendy W Chapman, Shawn J DeFries, Michael J Becich, Brian E Chapman

      Journal of Pathology Informatics 2010 1(1):24-24

      Background: Clinical records are often unstructured, free-text documents that create information extraction challenges and costs. Healthcare delivery and research organizations, such as the National Mesothelioma Virtual Bank, require the aggregation of both structured and unstructured data types. Natural language processing offers techniques for automatically extracting information from unstructured, free-text documents. Methods: Five hundred and eight history and physical reports from mesothelioma patients were split into development (208) and test sets (300). A reference standard was developed and each report was annotated by experts with regard to the patient's personal history of ancillary cancer and family history of any cancer. The Hx application was developed to process reports, extract relevant features, perform reference resolution and classify them with regard to cancer history. Two methods, Dynamic-Window and ConText, for extracting information were evaluated. Hx's classification responses using each of the two methods were measured against the reference standard. The average Cohen's weighted kappa served as the human benchmark in evaluating the system. Results: Hx had a high overall accuracy, with each method, scoring 96.2%. F-measures using the Dynamic-Window and ConText methods were 91.8% and 91.6%, which were comparable to the human benchmark of 92.8%. For the personal history classification, Dynamic-Window scored highest with 89.2% and for the family history classification, ConText scored highest with 97.6%, in which both methods were comparable to the human benchmark of 88.3% and 97.2%, respectively. Conclusion: We evaluated an automated application's performance in classifying a mesothelioma patient's personal and family history of cancer from clinical reports. To do so, the Hx application must process reports, identify cancer concepts, distinguish the known mesothelioma from ancillary cancers, recognize negation, perform reference resolution and determine the experiencer. Results indicated that both information extraction methods tested were dependant on the domain-specific lexicon and negation extraction. We showed that the more general method, ConText, performed as well as our task-specific method. Although Dynamic-Window could be modified to retrieve other concepts, ConText is more robust and performs better on inconclusive concepts. Hx could greatly improve and expedite the process of extracting data from free-text, clinical records for a variety of research or healthcare delivery organizations.
      Citation: Journal of Pathology Informatics 2010 1(1):24-24
      PubDate: Mon,11 Oct 2010
      DOI: 10.4103/2153-3539.71065
      Issue No: Vol. 1, No. 1 (2010)
       
  • Improving the visualization and detection of tissue folds in whole slide
           images through color enhancement
    • Authors: Pinky A Bautista, Yukako Yagi
      Pages: 25 - 25
      Abstract: Pinky A Bautista, Yukako Yagi

      Journal of Pathology Informatics 2010 1(1):25-25

      Objective : The objective of this paper is to improve the visualization and detection of tissue folds, which are prominent among tissue slides, from the pre-scan image of a whole slide image by introducing a color enhancement method that enables the differentiation between fold and non-fold image pixels. Method: The weighted difference between the color saturation and luminance of the image pixels is used as shifting factor to the original RGB color of the image. Results: Application of the enhancement method to hematoxylin and eosin (H&E) stained images improves the visualization of tissue folds regardless of the colorimetric variations in the images. Detection of tissue folds after application of the enhancement also improves but the presence of nuclei, which are also stained dark like the folds, was found to sometimes affect the detection accuracy. Conclusion: The presence of tissue artifacts could affect the quality of whole slide images, especially that whole slide scanners select the focus points from the pre-scan image wherein the artifacts are indistinguishable from real tissue area. We have a presented in this paper an enhancement scheme that improves the visualization and detection of tissue folds from pre-scan images. Since the method works on the simulated pre-scan images its integration to the actual whole slide imaging process should also be possible.
      Citation: Journal of Pathology Informatics 2010 1(1):25-25
      PubDate: Sat,27 Nov 2010
      DOI: 10.4103/2153-3539.73320
      Issue No: Vol. 1, No. 1 (2010)
       
  • Informatics methods for laboratory evaluation of HPV ordering patterns
           with an example from a nationwide sample in the United States, 2003-2009
    • Authors: Brian H Shirts, Brian R Jackson
      Pages: 26 - 26
      Abstract: Brian H Shirts, Brian R Jackson

      Journal of Pathology Informatics 2010 1(1):26-26

      Background: Laboratory data is a rich source of information that can be used to estimate adherence to physician guidelines and motivate improvement in clinical practice. Human papillomavirus (HPV) testing is an important component of cervical cancer screening programs with established screening guidelines. The purpose of this study was to develop methods to estimate concordance with published guidelines for HPV testing in order to provide clinicians and payors specific feedback about overscreening. Methods: This retrospective analysis of laboratory test ordering patterns evaluated 454,532 HPV tests ordered from September 2003 to October 2009 from 110 facilities and performed at ARUP laboratories. We used laboratory data including patient demographics, ordering frequency, timestamps and results to examine the proportion of HPV tests ordered on women under 21 years, ordered on women between 21 and 29 years apparently before cytological examination, repeated less than 1 year after a positive HPV result in women over 30 years, and repeated less than 3 years after a negative HPV result in women over 30 years. Results: The absolute number and proportion of HPV tests performed on women under 21 years declined from 20% in 2005 to 5% in October 2009. The proportion of HPV tests performed women between 21 and 29 years also declined during this period. Approximately one-third of HPV tests performed on women between 21 and 29 years arrived for HPV testing before cervical screening had presumably been completed. The most common follow-up intervals for HPV testing on women over 30 years were 6 months following a positive HPV result and 12 months following a negative HPV result. Only 6% of repeat HPV testing in women over 30 years followed a negative HPV result by 3 years or more. Approximately one-fourth of HPV tests ordered the year ending October 2009 were unnecessary based on the American Society for Colposcopy and Cervical Pathology guideline. Conclusions: We demonstrate simple methods to evaluate appropriate utilization of HPV testing using laboratory data. Our data illustrates that some aspects of HPV test ordering have become more consistent with guidelines over time. However, a large portion of HPV testing in the United States is unnecessary. This highlights opportunities for optimization of a rational cancer prevention strategy to reduce unnecessary screening, colposcopy and biopsies.
      Citation: Journal of Pathology Informatics 2010 1(1):26-26
      PubDate: Fri,3 Dec 2010
      DOI: 10.4103/2153-3539.73504
      Issue No: Vol. 1, No. 1 (2010)
       
  • Lewis Paul D: R for Medicine and Biology
    • Authors: G William Moore
      Pages: 27 - 27
      Abstract: G William Moore

      Journal of Pathology Informatics 2010 1(1):27-27


      Citation: Journal of Pathology Informatics 2010 1(1):27-27
      PubDate: Fri,3 Dec 2010
      DOI: 10.4103/2153-3539.73505
      Issue No: Vol. 1, No. 1 (2010)
       
  • The coming wave of change: ICD-10
    • Authors: Ji Yeon Kim, Bruce A Beckwith
      Pages: 28 - 28
      Abstract: Ji Yeon Kim, Bruce A Beckwith

      Journal of Pathology Informatics 2010 1(1):28-28


      Citation: Journal of Pathology Informatics 2010 1(1):28-28
      PubDate: Thu,23 Dec 2010
      DOI: 10.4103/2153-3539.74183
      Issue No: Vol. 1, No. 1 (2010)
       
  • Using image analysis as a tool for assessment of prognostic and predictive
           biomarkers for breast cancer: How reliable is it?
    • Authors: Mark C Lloyd, Pushpa Allam-Nandyala, Chetna N Purohit, Nancy Burke, Domenico Coppola, Marilyn M Bui
      Pages: 29 - 29
      Abstract: Mark C Lloyd, Pushpa Allam-Nandyala, Chetna N Purohit, Nancy Burke, Domenico Coppola, Marilyn M Bui

      Journal of Pathology Informatics 2010 1(1):29-29

      Background : Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) are important and well-established prognostic and predictive biomarkers for breast cancers and routinely tested on patient's tumor samples by immunohistochemical (IHC) study. The accuracy of these test results has substantial impact on patient management. A critical factor that contributes to the result is the interpretation (scoring) of IHC. This study investigates how computerized image analysis can play a role in a reliable scoring, and identifies potential pitfalls with common methods. Materials and Methods : Whole slide images of 33 invasive ductal carcinoma (IDC) (10 ER and 23 HER2) were scored by pathologist under the light microscope and confirmed by another pathologist. The HER2 results were additionally confirmed by fluorescence in situ hybridization (FISH). The scoring criteria were adherent to the guidelines recommended by the American Society of Clinical Oncology/College of American Pathologists. Whole slide stains were then scored by commercially available image analysis algorithms from Definiens (Munich, Germany) and Aperio Technologies (Vista, CA, USA). Each algorithm was modified specifically for each marker and tissue. The results were compared with the semi-quantitative manual scoring, which was considered the gold standard in this study. Results : For HER2 positive group, each algorithm scored 23/23 cases within the range established by the pathologist. For ER, both algorithms scored 10/10 cases within range. The performance of each algorithm varies somewhat from the percentage of staining as compared to the pathologist's reading. Conclusions : Commercially available computerized image analysis can be useful in the evaluation of ER and HER2 IHC results. In order to achieve accurate results either manual pathologist region selection is necessary, or an automated region selection tool must be employed. Specificity can also be gained when strict quality assurance by a pathologist is invested. Quality assurance of image analysis by pathologists is always warranted. Automated image analysis should only be used as adjunct to pathologist's evaluation.
      Citation: Journal of Pathology Informatics 2010 1(1):29-29
      PubDate: Thu,23 Dec 2010
      DOI: 10.4103/2153-3539.74186
      Issue No: Vol. 1, No. 1 (2010)
       
  • Abstracts
    • Pages: 12 - 12
      Abstract:

      Journal of Pathology Informatics 2014 5(1):12-12


      Citation: Journal of Pathology Informatics 2014 5(1):12-12
      PubDate: Mon,1 Jan 1900
      Issue No: Vol. 5, No. 1 (1900)
       
 
 
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