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Journal Cover Journal of Pathology Informatics
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  This is an Open Access Journal Open Access journal
   ISSN (Print) 2153-3539 - ISSN (Online) 2153-3539
   Published by Medknow Publishers Homepage  [305 journals]
  • Quantitative nucleic features are effective for discrimination of
           intraductal proliferative lesions of the breast

    • Authors: Masatoshi Yamada, Akira Saito, Yoichiro Yamamoto, Eric Cosatto, Atsushi Kurata, Toshitaka Nagao, Ayako Tateishi, Masahiko Kuroda
      Pages: 1 - 1
      Abstract: Masatoshi Yamada, Akira Saito, Yoichiro Yamamoto, Eric Cosatto, Atsushi Kurata, Toshitaka Nagao, Ayako Tateishi, Masahiko Kuroda

      Journal of Pathology Informatics 2016 7(1):1-1

      Background: Intraductal proliferative lesions (IDPLs) of the breast are recognized as a risk factor for subsequent invasive carcinoma development. Although opportunities for IDPL diagnosis have increased, these lesions are difficult to diagnose correctly, especially atypical ductal hyperplasia (ADH) and low-grade ductal carcinoma in situ (LG-DCIS). In order to define the difference between these lesions, many molecular pathological approaches have been performed. However, still we do not have a molecular marker and objective histological index about IDPLs of the breast. Methods: We generated full digital pathology archives from 175 female IDPL patients, including usual ductal hyperplasia (UDH), ADH, LG-DCIS, intermediate-grade (IM)-DCIS, and high-grade (HG)-DCIS. After total 2,035,807 nucleic segmentations were extracted, we evaluated nuclear features using step-wise linear discriminant analysis (LDA) and a support vector machine. Results: High diagnostic accuracy (81.8–99.3%) was achieved between pathologists' diagnoses and two-group LDA predictions from nucleic features for IDPL discrimination. Grouping of nuclear features as size and shape-related or intranuclear texture-related revealed that the latter group was more important when distinguishing between normal duct, UDH, ADH, and LG-DCIS. However, these two groups were equally important when discriminating between LG-DCIS and HG-DCIS. The Mahalanobis distances between each group showed that the smallest distance values occurred between LG-DCIS and IM-DCIS and between ADH and Normal. On the other hand, the distance value between ADH and LG-DCIS was larger than this distance. Conclusions: In this study, we have presented a practical and useful digital pathological method that incorporates nuclear morphological and textural features for IDPL prediction. We expect that this novel algorithm is used for the automated diagnosis assisting system for breast cancer.
      Citation: Journal of Pathology Informatics 2016 7(1):1-1
      PubDate: Fri,29 Jan 2016
      DOI: 10.4103/2153-3539.175380
      Issue No: Vol. 7, No. 1 (2016)
       
  • How can we improve Science, Technology, Engineering, and Math education to
           encourage careers in Biomedical and Pathology Informatics?

    • Authors: Rahul Uppal, Gunasheil Mandava, Katrina M Romagnoli, Andrew J King, Amie J Draper, Adam L Handen, Arielle M Fisher, Michael J Becich, Joyeeta Dutta-Moscato
      Pages: 2 - 2
      Abstract: Rahul Uppal, Gunasheil Mandava, Katrina M Romagnoli, Andrew J King, Amie J Draper, Adam L Handen, Arielle M Fisher, Michael J Becich, Joyeeta Dutta-Moscato

      Journal of Pathology Informatics 2016 7(1):2-2

      The Computer Science, Biology, and Biomedical Informatics (CoSBBI) program was initiated in 2011 to expose the critical role of informatics in biomedicine to talented high school students.[1] By involving them in Science, Technology, Engineering, and Math (STEM) training at the high school level and providing mentorship and research opportunities throughout the formative years of their education, CoSBBI creates a research infrastructure designed to develop young informaticians. Our central premise is that the trajectory necessary to be an expert in the emerging fields of biomedical informatics and pathology informatics requires accelerated learning at an early age.In our 4th year of CoSBBI as a part of the University of Pittsburgh Cancer Institute (UPCI) Academy (http://www.upci.upmc.edu/summeracademy/), and our 2nd year of CoSBBI as an independent informatics-based academy, we enhanced our classroom curriculum, added hands-on computer science instruction, and expanded research projects to include clinical informatics. We also conducted a qualitative evaluation of the program to identify areas that need improvement in order to achieve our goal of creating a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics in the era of big data and personalized medicine.
      Citation: Journal of Pathology Informatics 2016 7(1):2-2
      PubDate: Fri,29 Jan 2016
      DOI: 10.4103/2153-3539.175375
      Issue No: Vol. 7, No. 1 (2016)
       
  • Oxygen supply maps for hypoxic microenvironment visualization in prostate
           cancer

    • Authors: Niels J Rupp, Peter J Schuffler, Qing Zhong, Florian Falkner, Markus Rechsteiner, Jan H Ruschoff, Christian Fankhauser, Matthias Drach, Remo Largo, Mathias Tremp, Cedric Poyet, Tullio Sulser, Glen Kristiansen, Holger Moch, Joachim Buhmann, Michael Muntener, Peter J Wild
      Pages: 3 - 3
      Abstract: Niels J Rupp, Peter J Schuffler, Qing Zhong, Florian Falkner, Markus Rechsteiner, Jan H Ruschoff, Christian Fankhauser, Matthias Drach, Remo Largo, Mathias Tremp, Cedric Poyet, Tullio Sulser, Glen Kristiansen, Holger Moch, Joachim Buhmann, Michael Muntener, Peter J Wild

      Journal of Pathology Informatics 2016 7(1):3-3

      Background: Intratumoral hypoxia plays an important role with regard to tumor biology and susceptibility to radio. and chemotherapy. For further investigation of hypoxia.related changes, areas of certain hypoxia must be reliably detected within cancer tissues. Pimonidazole, a 2.nitroimindazole, accumulates in hypoxic tissue and can be easily visualized using immunohistochemistry. Materials and Methods: To improve detection of highly hypoxic versus normoxic areas in prostate cancer, immunoreactivity of pimonidazole and a combination of known hypoxia.related proteins was used to create computational oxygen supply maps of prostate cancer. Pimonidazole was intravenously administered before radical prostatectomy in n = 15 patients, using the da Vinci robot.assisted surgical system. Prostatectomy specimens were immediately transferred into buffered formaldehyde, fixed overnight, and completely embedded in paraffin. Pimonidazole accumulation and hypoxia.related protein expression were visualized by immunohistochemistry. Oxygen supply maps were created using the normalized information from pimonidazole and hypoxia.related proteins. Results: Based on pimonidazole staining and other hypoxia.related proteins (osteopontin, hypoxia.inducible factor 1.alpha, and glucose transporter member 1) oxygen supply maps in prostate cancer were created. Overall, oxygen supply maps consisting of information from all hypoxia.related proteins showed high correlation and mutual information to the golden standard of pimonidazole. Here, we describe an improved computer.based ex vivo model for an accurate detection of oxygen supply in human prostate cancer tissue. Conclusions: This platform can be used for precise colocalization of novel candidate hypoxia.related proteins in a representative number of prostate cancer cases, and improve issues of single marker correlations. Furthermore, this study provides a source for further in situ tests and biochemical investigations
      Citation: Journal of Pathology Informatics 2016 7(1):3-3
      PubDate: Fri,29 Jan 2016
      DOI: 10.4103/2153-3539.175376
      Issue No: Vol. 7, No. 1 (2016)
       
  • Diagnostic time in digital pathology: A comparative study on 400 cases

    • Authors: Aleksandar Vodovnik
      Pages: 4 - 4
      Abstract: Aleksandar Vodovnik

      Journal of Pathology Informatics 2016 7(1):4-4

      Background: Numerous validation studies in digital pathology confirmed its value as a diagnostic tool. However, a longer time to diagnosis than traditional microscopy has been seen as a significant barrier to the routine use of digital pathology. As a part of our validation study, we compared a digital and microscopic diagnostic time in the routine diagnostic setting. Materials and Methods: One senior staff pathologist reported 400 consecutive cases in histology, nongynecological, and fine needle aspiration cytology (20 sessions, 20 cases/session), over 4 weeks. Complex, difficult, and rare cases were excluded from the study to reduce the bias. A primary diagnosis was digital, followed by traditional microscopy, 6 months later, with only request forms available for both. Microscopic slides were scanned at ×20, digital images accessed through the fully integrated laboratory information management system (LIMS) and viewed in the image viewer on double 23” displays. A median broadband speed was 299 Mbps. A diagnostic time was measured from the point slides were made available to the point diagnosis was made or additional investigations were deemed necessary, recorded independently in minutes/session and compared. Results: A digital diagnostic time was 1841 and microscopic 1956 min; digital being shorter than microscopic in 13 sessions. Four sessions with shorter microscopic diagnostic time included more cases requiring extensive use of magnifications over ×20. Diagnostic time was similar in three sessions. Conclusions: A diagnostic time in digital pathology can be shorter than traditional microscopy in the routine diagnostic setting, with adequate and stable network speeds, fully integrated LIMS and double displays as default parameters. This also related to better ergonomics, larger viewing field, and absence of physical slide handling, with effects on both diagnostic and nondiagnostic time. Differences with previous studies included a design, image size, number of cases, specimen type, network speed, and participant's level of confidence and experience in digital reporting. Further advancements in working stations and gained experience in digital reporting are expected to improve diagnostic time and widen routine applications of digital pathology.
      Citation: Journal of Pathology Informatics 2016 7(1):4-4
      PubDate: Fri,29 Jan 2016
      DOI: 10.4103/2153-3539.175377
      Issue No: Vol. 7, No. 1 (2016)
       
  • Feature-based analysis of mouse prostatic intraepithelial neoplasia in
           histological tissue sections

    • Authors: Pekka Ruusuvuori, Mira Valkonen, Matti Nykter, Tapio Visakorpi, Leena Latonen
      Pages: 5 - 5
      Abstract: Pekka Ruusuvuori, Mira Valkonen, Matti Nykter, Tapio Visakorpi, Leena Latonen

      Journal of Pathology Informatics 2016 7(1):5-5

      This paper describes work presented at the Nordic Symposium on Digital Pathology 2015, in Linköping, Sweden. Prostatic intraepithelial neoplasia (PIN) represents premalignant tissue involving epithelial growth confined in the lumen of prostatic acini. In the attempts to understand oncogenesis in the human prostate, early neoplastic changes can be modeled in the mouse with genetic manipulation of certain tumor suppressor genes or oncogenes. As with many early pathological changes, the PIN lesions in the mouse prostate are macroscopically small, but microscopically spanning areas often larger than single high magnification focus fields in microscopy. This poses a challenge to utilize full potential of the data acquired in histological specimens. We use whole prostates fixed in molecular fixative PAXgene™, embedded in paraffin, sectioned through and stained with H&E. To visualize and analyze the microscopic information spanning whole mouse PIN (mPIN) lesions, we utilize automated whole slide scanning and stacked sections through the tissue. The region of interests is masked, and the masked areas are processed using a cascade of automated image analysis steps. The images are normalized in color space, after which exclusion of secretion areas and feature extraction is performed. Machine learning is utilized to build a model of early PIN lesions for determining the probability for histological changes based on the calculated features. We performed a feature-based analysis to mPIN lesions. First, a quantitative representation of over 100 features was built, including several features representing pathological changes in PIN, especially describing the spatial growth pattern of lesions in the prostate tissue. Furthermore, we built a classification model, which is able to align PIN lesions corresponding to grading by visual inspection to more advanced and mild lesions. The classifier allowed both determining the probability of early histological changes for uncategorized tissue samples and interpretation of the model parameters. Here, we develop quantitative image analysis pipeline to describe morphological changes in histological images. Even subtle changes in mPIN lesion characteristics can be described with feature analysis and machine learning. Constructing and using multidimensional feature data to represent histological changes enables richer analysis and interpretation of early pathological lesions.
      Citation: Journal of Pathology Informatics 2016 7(1):5-5
      PubDate: Fri,29 Jan 2016
      DOI: 10.4103/2153-3539.175378
      Issue No: Vol. 7, No. 1 (2016)
       
  • Data security in genomics: A review of Australian privacy requirements and
           their relation to cryptography in data storage

    • Authors: Arran Schlosberg
      Pages: 6 - 6
      Abstract: Arran Schlosberg

      Journal of Pathology Informatics 2016 7(1):6-6

      The advent of next-generation sequencing (NGS) brings with it a need to manage large volumes of patient data in a manner that is compliant with both privacy laws and long-term archival needs. Outside of the realm of genomics there is a need in the broader medical community to store data, and although radiology aside the volume may be less than that of NGS, the concepts discussed herein are similarly relevant. The relation of so-called "privacy principles" to data protection and cryptographic techniques is explored with regards to the archival and backup storage of health data in Australia, and an example implementation of secure management of genomic archives is proposed with regards to this relation. Readers are presented with sufficient detail to have informed discussions - when implementing laboratory data protocols - with experts in the fields.
      Citation: Journal of Pathology Informatics 2016 7(1):6-6
      PubDate: Fri,5 Feb 2016
      DOI: 10.4103/2153-3539.175793
      Issue No: Vol. 7, No. 1 (2016)
       
  • Implementation of Epic Beaker Clinical Pathology at an academic medical
           center

    • Authors: Matthew D Krasowski, Joseph D Wilford, Wanita Howard, Susan K Dane, Scott R Davis, Nitin J Karandikar, John L Blau, Bradley A Ford
      Pages: 7 - 7
      Abstract: Matthew D Krasowski, Joseph D Wilford, Wanita Howard, Susan K Dane, Scott R Davis, Nitin J Karandikar, John L Blau, Bradley A Ford

      Journal of Pathology Informatics 2016 7(1):7-7

      Background: Epic Beaker Clinical Pathology (CP) is a relatively new laboratory information system (LIS) operating within the Epic suite of software applications. To date, there have not been any publications describing implementation of Beaker CP. In this report, we describe our experience in implementing Beaker CP version 2012 at a state academic medical center with a go-live of August 2014 and a subsequent upgrade to Beaker version 2014 in May 2015. The implementation of Beaker CP was concurrent with implementations of Epic modules for revenue cycle, patient scheduling, and patient registration. Methods: Our analysis covers approximately 3 years of time (2 years preimplementation of Beaker CP and roughly 1 year after) using data summarized from pre- and post-implementation meetings, debriefings, and the closure document for the project. Results: We summarize positive aspects of, and key factors leading to, a successful implementation of Beaker CP. The early inclusion of subject matter experts in the design and validation of Beaker workflows was very helpful. Since Beaker CP does not directly interface with laboratory instrumentation, the clinical laboratories spent extensive preimplementation effort establishing middleware interfaces. Immediate challenges postimplementation included bar code scanning and nursing adaptation to Beaker CP specimen collection. The most substantial changes in laboratory workflow occurred with microbiology orders. This posed a considerable challenge with microbiology orders from the operating rooms and required intensive interventions in the weeks following go-live. In postimplementation surveys, pathology staff, informatics staff, and end-users expressed satisfaction with the new LIS. Conclusions: Beaker CP can serve as an effective LIS for an academic medical center. Careful planning and preparation aid the transition to this LIS.
      Citation: Journal of Pathology Informatics 2016 7(1):7-7
      PubDate: Fri,5 Feb 2016
      DOI: 10.4103/2153-3539.175798
      Issue No: Vol. 7, No. 1 (2016)
       
  • Utilization of virtual microscopy in cytotechnology educational programs
           in the United States

    • Authors: Maheswari S Mukherjee, Amber D Donnelly, Vincent J DeAgano, Elizabeth R Lyden, Stanley J Radio
      Pages: 8 - 8
      Abstract: Maheswari S Mukherjee, Amber D Donnelly, Vincent J DeAgano, Elizabeth R Lyden, Stanley J Radio

      Journal of Pathology Informatics 2016 7(1):8-8

      Background: Our cytotechnology (CT) program has been utilizing virtual microscopy (VM) as an adjunct educational resource since 2011. Aims: The aim of this study was to identify the utilization of VM in other CT programs across the United States (US). Subjects and Methods: A cover letter was sent to the program directors of all accredited CT programs in the US (excluding our program), requesting their participation in an online survey. After 2 days, the participants were sent an online link to the survey. The survey results were analyzed using descriptive statistics. Results: There were a total of 25 respondents to the survey. Among the 25, three CT programs use VM. Two of the three programs have been using VM for
      Citation: Journal of Pathology Informatics 2016 7(1):8-8
      PubDate: Tue,1 Mar 2016
      DOI: 10.4103/2153-3539.177682
      Issue No: Vol. 7, No. 1 (2016)
       
  • Commentary: Can pathologists interpret digital images as well as they
           interpret microscope slides?

    • Authors: Thomas W Bauer
      Pages: 9 - 9
      Abstract: Thomas W Bauer

      Journal of Pathology Informatics 2016 7(1):9-9


      Citation: Journal of Pathology Informatics 2016 7(1):9-9
      PubDate: Tue,1 Mar 2016
      DOI: 10.4103/2153-3539.177683
      Issue No: Vol. 7, No. 1 (2016)
       
  • Comparison of the diagnostic utility of digital pathology systems for
           telemicrobiology

    • Authors: Daniel D Rhoads, Nadia F Habib-Bein, Rahman S Hariri, Douglas J Hartman, Sara E Monaco, Andrew Lesniak, Jon Duboy, Mohamed El-Sayed Salama, Liron Pantanowitz
      Pages: 10 - 10
      Abstract: Daniel D Rhoads, Nadia F Habib-Bein, Rahman S Hariri, Douglas J Hartman, Sara E Monaco, Andrew Lesniak, Jon Duboy, Mohamed El-Sayed Salama, Liron Pantanowitz

      Journal of Pathology Informatics 2016 7(1):10-10

      Introduction: Telemicrobiology is a growing component of clinical microbiology informatics. However, few studies have been performed to assess the diagnostic utility of telemicroscopy systems in evaluating infectious agents. Objective: Evaluate multiple contemporary digital pathology platforms for use in diagnostic telemicrobiology. Materials and Methods: A mix of thirty cases that included viral, bacterial, fungal, and parasitological findings were evaluated by four experts using ×40 whole slide imaging (WSI) scans, ×83 oil-immersion WSI scans, ×100 oil-immersion WSI scans, digital photomicrographs, and glass slides. Results: The ×83 WSI, ×100 WSI, and photomicrograph interpretations were not significantly different in quality and accuracy when compared to glass slide interpretations. The ×40 WSI interpretations were of lower quality and were more likely to be incorrect when compared to glass slide interpretations. Conclusions: In this study, high magnification, oil-immersion digital pathology platforms are better suited to support telemicrobiology applications and yield interpretations on par with glass slide evaluations.
      Citation: Journal of Pathology Informatics 2016 7(1):10-10
      PubDate: Tue,1 Mar 2016
      DOI: 10.4103/2153-3539.177687
      Issue No: Vol. 7, No. 1 (2016)
       
  • Consultation on urological specimens from referred cancer patients using
           real-time digital microscopy: Optimizing the workflow

    • Pages: 11 - 11
      Abstract: Henrik Holten-Rossing, Lise Grupe Larsen, Birgitte Grønkær Toft, Anand Loya, Ben Vainer

      Journal of Pathology Informatics 2016 7(1):11-11

      Introduction: Centralization of cancer treatment entails a reassessment of the diagnostic tissue specimens. Packaging and shipment of glass slides from the local to the central pathology unit means that the standard procedure is time-consuming and that it is difficult to comply with governmental requirements. The aim was to evaluate whether real-time digital microscopy for urological cancer specimens during the primary diagnostic process can replace subsequent physical slide referral and reassessment without compromising diagnostic safety. Methods: From May to October 2014, tissue specimens from 130 patients with urological cancer received at Næstved Hospital's Pathology Department, and expected to be referred for further treatment at cancer unit of a university hospital, were diagnosed using standard light microscopy. In the event of diagnostic uncertainty, the VisionTek digital microscope (Sakura Finetek) was employed. The Pathology Department at Næstved Hospital was equipped with a digital microscope and three consultant pathologists were stationed at Rigshospitalet with workstations optimized for digital microscopy. Representative slides for each case were selected for consultation and live digital consultation took place over the telephone using remote access software. Time of start and finish for each case was logged. For the physically referred cases, time from arrival to sign-out was logged in the national pathology information system, and time spent on microscopy and reporting was noted manually. Diagnosis, number of involved biopsies, grade, and stage were compared between digital microscopy and conventional microscopy. Results: Complete data were available for all 130 cases. Standard procedure with referral of urological cancer specimens took a mean of 8 min 56 s for microscopy, reporting and sign-out per case. For live digital consultations, a mean of 18 min 37 s was spent on each consultation with 4 min 43 s for each case, depending on the number of digital slides included. Only in two cases could a consensus regarding the diagnosis not be reached during live consultation; this did not, it should be noted, affect patient treatment. Complete agreement between conventional and digital histopathology diagnosis was reached in all the 53 patients referred to central pathology units. The participating pathologists were in general comfortable using live digital microscopy, but they emphasized that a fast internet connection was essential for a smooth consultation. Discussion and Conclusion: An almost perfect agreement between live digital and conventional microscopy was observed in this study. Live digital consultation allowed cases to be referred from local hospitals to central cancer units without the standard delay caused by shipment. Only a few preselected specimen slides for each patient were presented in live consultation, which reduced the time spent on diagnosis compared to using the conventional method. Implementation of real-time digital microscopy would result in quicker turnaround and patient referral time, and with careful selection of relevant specimen slides for consultation, diagnostic safety would not be compromised.
      Citation: Journal of Pathology Informatics 2016 7(1):11-11
      PubDate: Tue,1 Mar 2016
      DOI: 10.4103/2153-3539.177689
      Issue No: Vol. 7, No. 1 (2016)
       
  • Summary of third Nordic symposium on digital pathology

    • Authors: Claes Lundstrom, Marie Waltersson, Anders Persson, Darren Treanor
      Pages: 12 - 12
      Abstract: Claes Lundstrom, Marie Waltersson, Anders Persson, Darren Treanor

      Journal of Pathology Informatics 2016 7(1):12-12

      Cross-disciplinary and cross-sectorial collaboration is a key success factor for turning the promise of digital pathology into actual clinical benefits. The Nordic symposium on digital pathology (NDP) was created to promote knowledge exchange in this area, among stakeholders in health care, industry, and academia. This article is a summary of the third NDP symposium in Linkφping, Sweden. The Nordic experiences, including several hospitals using whole-slide imaging for substantial parts of their primary reviews, formed a fertile base for discussions among the 190 NDP attendees originating from 15 different countries. This summary also contains results from a survey on adoption and validation aspects of clinical digital pathology use.
      Citation: Journal of Pathology Informatics 2016 7(1):12-12
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179902
      Issue No: Vol. 7, No. 1 (2016)
       
  • Pathology interface for the molecular analysis of tissue by mass
           spectrometry

    • Authors: Jeremy L Norris, Tina Tsui, Danielle B Gutierrez, Richard M Caprioli
      Pages: 13 - 13
      Abstract: Jeremy L Norris, Tina Tsui, Danielle B Gutierrez, Richard M Caprioli

      Journal of Pathology Informatics 2016 7(1):13-13

      Background: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established. Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images. Results: We describe a microscopy-driven approach to tissue analysis by IMS. Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.
      Citation: Journal of Pathology Informatics 2016 7(1):13-13
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179903
      Issue No: Vol. 7, No. 1 (2016)
       
  • Perceptions of pathology informatics by non-informaticist pathologists and
           trainees

    • Authors: Addie Walker, Christopher Garcia, Jason M Baron, Thomas M Gudewicz, John R Gilbertson, Walter H Henricks, Roy E Lee
      Pages: 14 - 14
      Abstract: Addie Walker, Christopher Garcia, Jason M Baron, Thomas M Gudewicz, John R Gilbertson, Walter H Henricks, Roy E Lee

      Journal of Pathology Informatics 2016 7(1):14-14

      Background: Although pathology informatics (PI) is essential to modern pathology practice, the field is often poorly understood. Pathologists who have received little to no exposure to informatics, either in training or in practice, may not recognize the roles that informatics serves in pathology. The purpose of this study was to characterize perceptions of PI by noninformatics-oriented pathologists and to do so at two large centers with differing informatics environments. Methods: Pathology trainees and staff at Cleveland Clinic (CC) and Massachusetts General Hospital (MGH) were surveyed. At MGH, pathology department leadership has promoted a pervasive informatics presence through practice, training, and research. At CC, PI efforts focus on production systems that serve a multi-site integrated health system and a reference laboratory, and on the development of applications oriented to department operations. The survey assessed perceived definition of PI, interest in PI, and perceived utility of PI. Results: The survey was completed by 107 noninformatics-oriented pathologists and trainees. A majority viewed informatics positively. Except among MGH trainees, confusion of PI with information technology (IT) and help desk services was prominent, even in those who indicated they understood informatics. Attendings and trainees indicated desire to learn more about PI. While most acknowledged that having some level of PI knowledge would be professionally useful and advantageous, only a minority plan to utilize it. Conclusions: Informatics is viewed positively by the majority of noninformatics pathologists at two large centers with differing informatics orientations. Differences in departmental informatics culture can be attributed to the varying perceptions of PI by different individuals. Incorrect perceptions exist, such as conflating PI with IT and help desk services, even among those who claim to understand PI. Further efforts by the PI community could address such misperceptions, which could help enable a better understanding of what PI is and is not, and potentially lead to increased acceptance by non-informaticist pathologists.
      Citation: Journal of Pathology Informatics 2016 7(1):14-14
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179904
      Issue No: Vol. 7, No. 1 (2016)
       
  • Quantitative analysis of myocardial tissue with digital autofluorescence
           microscopy

    • Authors: Thomas Jensen, Henrik Holten-Rossing, Ida M H Svendsen, Christina Jacobsen, Ben Vainer
      Pages: 15 - 15
      Abstract: Thomas Jensen, Henrik Holten-Rossing, Ida M H Svendsen, Christina Jacobsen, Ben Vainer

      Journal of Pathology Informatics 2016 7(1):15-15

      Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.
      Citation: Journal of Pathology Informatics 2016 7(1):15-15
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179908
      Issue No: Vol. 7, No. 1 (2016)
       
  • Review of "Practical Informatics for Cytopathology"

    • Authors: George G Birdsong
      Pages: 16 - 16
      Abstract: George G Birdsong

      Journal of Pathology Informatics 2016 7(1):16-16


      Citation: Journal of Pathology Informatics 2016 7(1):16-16
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179909
      Issue No: Vol. 7, No. 1 (2016)
       
  • Empirical comparison of color normalization methods for epithelial-stromal
           classification in H and E images

    • Authors: Amit Sethi, Lingdao Sha, Abhishek Ramnath Vahadane, Ryan J Deaton, Neeraj Kumar, Virgilia Macias, Peter H Gann
      Pages: 17 - 17
      Abstract: Amit Sethi, Lingdao Sha, Abhishek Ramnath Vahadane, Ryan J Deaton, Neeraj Kumar, Virgilia Macias, Peter H Gann

      Journal of Pathology Informatics 2016 7(1):17-17

      Context: Color normalization techniques for histology have not been empirically tested for their utility for computational pathology pipelines. Aims: We compared two contemporary techniques for achieving a common intermediate goal - epithelial-stromal classification. Settings and Design: Expert-annotated regions of epithelium and stroma were treated as ground truth for comparing classifiers on original and color-normalized images. Materials and Methods: Epithelial and stromal regions were annotated on thirty diverse-appearing H and E stained prostate cancer tissue microarray cores. Corresponding sets of thirty images each were generated using the two color normalization techniques. Color metrics were compared for original and color-normalized images. Separate epithelial-stromal classifiers were trained and compared on test images. Main analyses were conducted using a multiresolution segmentation (MRS) approach; comparative analyses using two other classification approaches (convolutional neural network [CNN], Wndchrm) were also performed. Statistical Analysis: For the main MRS method, which relied on classification of super-pixels, the number of variables used was reduced using backward elimination without compromising accuracy, and test - area under the curves (AUCs) were compared for original and normalized images. For CNN and Wndchrm, pixel classification test-AUCs were compared. Results: Khan method reduced color saturation while Vahadane reduced hue variance. Super-pixel-level test-AUC for MRS was 0.010-0.025 (95% confidence interval limits ± 0.004) higher for the two normalized image sets compared to the original in the 10-80 variable range. Improvement in pixel classification accuracy was also observed for CNN and Wndchrm for color-normalized images. Conclusions: Color normalization can give a small incremental benefit when a super-pixel-based classification method is used with features that perform implicit color normalization while the gain is higher for patch-based classification methods for classifying epithelium versus stroma.
      Citation: Journal of Pathology Informatics 2016 7(1):17-17
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.179984
      Issue No: Vol. 7, No. 1 (2016)
       
  • An industry perspective: An update on the adoption of whole slide imaging

    • Authors: Michael C Montalto
      Pages: 18 - 18
      Abstract: Michael C Montalto

      Journal of Pathology Informatics 2016 7(1):18-18

      This manuscript is an adaptation of the closing keynote presentation of the Digital Pathology Association Pathology Visions Conference 2015 in Boston, MA, USA. In this presentation, analogies are drawn between the adoption of whole slide imaging (WSI) and other mainstream digital technologies, including digital music and books. In doing so, it is revealed that the adoption of seemingly similar digital technologies does not follow the same adoption profiles and that understanding the unique aspects of value for each customer segment is critical. Finally, a call to action is given to academia and industry to study the value that WSI brings to the global healthcare community.
      Citation: Journal of Pathology Informatics 2016 7(1):18-18
      PubDate: Mon,11 Apr 2016
      DOI: 10.4103/2153-3539.180014
      Issue No: Vol. 7, No. 1 (2016)
       
  • Commentary: Has pathology gone to the "birds" because we have
           just been "winging" it?

    • Authors: Liron Pantanowitz, Eric Glassy
      Pages: 19 - 19
      Abstract: Liron Pantanowitz, Eric Glassy

      Journal of Pathology Informatics 2016 7(1):19-19


      Citation: Journal of Pathology Informatics 2016 7(1):19-19
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181763
      Issue No: Vol. 7, No. 1 (2016)
       
  • Validation of break-apart and fusion MYC probes using a digital
           fluorescence in situ hybridization capture and imaging system

    • Authors: Michael Liew, Leslie Rowe, Parker W Clement, Rodney R Miles, Mohamed E Salama
      Pages: 20 - 20
      Abstract: Michael Liew, Leslie Rowe, Parker W Clement, Rodney R Miles, Mohamed E Salama

      Journal of Pathology Informatics 2016 7(1):20-20

      Introduction: Detection of MYC translocations using fluorescence in situ hybridization (FISH) is important in the evaluation of lymphomas, in particular, Burkitt lymphoma and diffuse large B-cell lymphoma. Our aim was to validate a digital FISH capture and imaging system for the detection of MYC 8q24 translocations using LSI-MYC (a break-apart probe) and MYC 8;14 translocation using IGH-MYC (a fusion probe). Materials and Methods: LSI-MYC probe was evaluated using tissue sections from 35 patients. IGH-MYC probe was evaluated using tissue sections from forty patients. Sections were processed for FISH and analyzed using traditional methods. FISH slides were then analyzed using the GenASIs capture and analysis system. Results: Results for LSI-MYC had a high degree of correlation between traditional method of FISH analysis and digital FISH analysis. Results for IGH-MYC had a 100% concordance between traditional method of FISH analysis and digital FISH analysis. Conclusion: Annotated whole slide images of H and E and FISH sections can be digitally aligned, so that areas of tumor within a section can be matched and evaluated with a greater degree of accuracy. Images can be archived permanently, providing a means for examining the results retrospectively. Digital FISH imaging of the MYC translocations provides a better diagnostic tool compared to traditional methods for evaluating lymphomas.
      Citation: Journal of Pathology Informatics 2016 7(1):20-20
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181764
      Issue No: Vol. 7, No. 1 (2016)
       
  • Removing defocused objects from single focal plane scans of cytological
           slides

    • Pages: 21 - 21
      Abstract: David Friedrich, Alfred Böcking, Dietrich Meyer-Ebrecht, Dorit Merhof

      Journal of Pathology Informatics 2016 7(1):21-21

      Background: Virtual microscopy and automated processing of cytological slides are more challenging compared to histological slides. Since cytological slides exhibit a three-dimensional surface and the required microscope objectives with high resolution have a low depth of field, these cannot capture all objects of a single field of view in focus. One solution would be to scan multiple focal planes; however, the increase in processing time and storage requirements are often prohibitive for clinical routine. Materials and Methods: In this paper, we show that it is a reasonable trade-off to scan a single focal plane and automatically reject defocused objects from the analysis. To this end, we have developed machine learning solutions for the automated identification of defocused objects. Our approach includes creating novel features, systematically optimizing their parameters, selecting adequate classifier algorithms, and identifying the correct decision boundary between focused and defocused objects. We validated our approach for computer-assisted DNA image cytometry. Results and Conclusions: We reach an overall sensitivity of 96.08% and a specificity of 99.63% for identifying defocused objects. Applied on ninety cytological slides, the developed classifiers automatically removed 2.50% of the objects acquired during scanning, which otherwise would have interfered the examination. Even if not all objects are acquired in focus, computer-assisted DNA image cytometry still identified more diagnostically or prognostically relevant objects compared to manual DNA image cytometry. At the same time, the workload for the expert is reduced dramatically.
      Citation: Journal of Pathology Informatics 2016 7(1):21-21
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181765
      Issue No: Vol. 7, No. 1 (2016)
       
  • Exploring virtual reality technology and the Oculus Rift for the
           examination of digital pathology slides

    • Authors: Navid Farahani, Robert Post, Jon Duboy, Ishtiaque Ahmed, Brian J Kolowitz, Teppituk Krinchai, Sara E Monaco, Jeffrey L Fine, Douglas J Hartman, Liron Pantanowitz
      Pages: 22 - 22
      Abstract: Navid Farahani, Robert Post, Jon Duboy, Ishtiaque Ahmed, Brian J Kolowitz, Teppituk Krinchai, Sara E Monaco, Jeffrey L Fine, Douglas J Hartman, Liron Pantanowitz

      Journal of Pathology Informatics 2016 7(1):22-22

      Background: Digital slides obtained from whole slide imaging (WSI) platforms are typically viewed in two dimensions using desktop personal computer monitors or more recently on mobile devices. To the best of our knowledge, we are not aware of any studies viewing digital pathology slides in a virtual reality (VR) environment. VR technology enables users to be artificially immersed in and interact with a computer-simulated world. Oculus Rift is among the world's first consumer-targeted VR headsets, intended primarily for enhanced gaming. Our aim was to explore the use of the Oculus Rift for examining digital pathology slides in a VR environment. Methods: An Oculus Rift Development Kit 2 (DK2) was connected to a 64-bit computer running Virtual Desktop software. Glass slides from twenty randomly selected lymph node cases (ten with benign and ten malignant diagnoses) were digitized using a WSI scanner. Three pathologists reviewed these digital slides on a 27-inch 5K display and with the Oculus Rift after a 2-week washout period. Recorded endpoints included concordance of final diagnoses and time required to examine slides. The pathologists also rated their ease of navigation, image quality, and diagnostic confidence for both modalities. Results: There was 90% diagnostic concordance when reviewing WSI using a 5K display and Oculus Rift. The time required to examine digital pathology slides on the 5K display averaged 39 s (range 10-120 s), compared to 62 s with the Oculus Rift (range 15-270 s). All pathologists confirmed that digital pathology slides were easily viewable in a VR environment. The ratings for image quality and diagnostic confidence were higher when using the 5K display. Conclusion: Using the Oculus Rift DK2 to view and navigate pathology whole slide images in a virtual environment is feasible for diagnostic purposes. However, image resolution using the Oculus Rift device was limited. Interactive VR technologies such as the Oculus Rift are novel tools that may be of use in digital pathology.
      Citation: Journal of Pathology Informatics 2016 7(1):22-22
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181766
      Issue No: Vol. 7, No. 1 (2016)
       
  • Digital pathology and anatomic pathology laboratory information system
           integration to support digital pathology sign-out

    • Pages: 23 - 23
      Abstract: Huazhang Guo, Joe Birsa, Navid Farahani, Douglas J Hartman, Anthony Piccoli, Matthew O'Leary, Jeffrey McHugh, Mark Nyman, Curtis Stratman, Vanja Kvarnstrom, Samuel Yousem, Liron Pantanowitz

      Journal of Pathology Informatics 2016 7(1):23-23

      Background: The adoption of digital pathology offers benefits over labor-intensive, time-consuming, and error-prone manual processes. However, because most workflow and laboratory transactions are centered around the anatomical pathology laboratory information system (APLIS), adoption of digital pathology ideally requires integration with the APLIS. A digital pathology system (DPS) integrated with the APLIS was recently implemented at our institution for diagnostic use. We demonstrate how such integration supports digital workflow to sign-out anatomical pathology cases. Methods: Workflow begins when pathology cases get accessioned into the APLIS (CoPathPlus). Glass slides from these cases are then digitized (Omnyx VL120 scanner) and automatically uploaded into the DPS (Omnyx; Integrated Digital Pathology (IDP) software v.1.3). The APLIS transmits case data to the DPS via a publishing web service. The DPS associates scanned images with the correct case using barcode labels on slides and information received from the APLIS. When pathologists remotely open a case in the DPS, additional information (e.g. gross pathology details, prior cases) gets retrieved from the APLIS through a query web service. Results: Following validation of this integration, pathologists at our institution have signed out more than 1000 surgical pathology cases in a production environment. Integration between the APLIS and DPS enabled pathologists to review digital slides while simultaneously having access to pertinent case metadata. The introduction of a digital workflow eliminated costly manual tasks involving matching of glass slides and avoided delays waiting for glass slides to be delivered. Conclusion: Integrating the DPS and APLIS were instrumental for successfully implementing a digital solution at our institution for pathology sign-out. The integration streamlined our digital sign-out workflow, diminished the potential for human error related to matching slides, and improved the sign-out experience for pathologists.
      Citation: Journal of Pathology Informatics 2016 7(1):23-23
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181767
      Issue No: Vol. 7, No. 1 (2016)
       
  • A real-time dashboard for managing pathology processes

    • Authors: Fawaz Halwani, Wei Chen Li, Diponkar Banerjee, Lysanne Lessard, Daniel Amyot, Wojtek Michalowski, Randy Giffen
      Pages: 24 - 24
      Abstract: Fawaz Halwani, Wei Chen Li, Diponkar Banerjee, Lysanne Lessard, Daniel Amyot, Wojtek Michalowski, Randy Giffen

      Journal of Pathology Informatics 2016 7(1):24-24

      Context: The Eastern Ontario Regional Laboratory Association (EORLA) is a newly established association of all the laboratory and pathology departments of Eastern Ontario that currently includes facilities from eight hospitals. All surgical specimens for EORLA are processed in one central location, the Department of Pathology and Laboratory Medicine (DPLM) at The Ottawa Hospital (TOH), where the rapid growth and influx of surgical and cytology specimens has created many challenges in ensuring the timely processing of cases and reports. Although the entire process is maintained and tracked in a clinical information system, this system lacks pre-emptive warnings that can help management address issues as they arise. Aims: Dashboard technology provides automated, real-time visual clues that could be used to alert management when a case or specimen is not being processed within predefined time frames. We describe the development of a dashboard helping pathology clinical management to make informed decisions on specimen allocation and tracking. Methods: The dashboard was designed and developed in two phases, following a prototyping approach. The first prototype of the dashboard helped monitor and manage pathology processes at the DPLM. Results: The use of this dashboard helped to uncover operational inefficiencies and contributed to an improvement of turn-around time within The Ottawa Hospital's DPML. It also allowed the discovery of additional requirements, leading to a second prototype that provides finer-grained, real-time information about individual cases and specimens. Conclusion: We successfully developed a dashboard that enables managers to address delays and bottlenecks in specimen allocation and tracking. This support ensures that pathology reports are provided within time frame standards required for high-quality patient care. Given the importance of rapid diagnostics for a number of diseases, the use of real-time dashboards within pathology departments could contribute to improving the quality of patient care beyond EORLA's.
      Citation: Journal of Pathology Informatics 2016 7(1):24-24
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181768
      Issue No: Vol. 7, No. 1 (2016)
       
  • Pitfalls in the use of whole slide imaging for the diagnosis of central
           nervous system tumors: A pilot study in surgical neuropathology

    • Authors: Melike Pekmezci, Sanem Pinar Uysal, Yelda Orhan, Tarik Tihan, Han Sung Lee
      Pages: 25 - 25
      Abstract: Melike Pekmezci, Sanem Pinar Uysal, Yelda Orhan, Tarik Tihan, Han Sung Lee

      Journal of Pathology Informatics 2016 7(1):25-25

      Background: Whole slide imaging (WSI) finds increasingly higher value in everyday surgical pathology in addition to its well-established use for educational and research purposes. However, its diagnostic utility, especially in subspecialty settings such as neuropathology, is not fully validated. Neuropathology practice is unique with smaller overall tissue size and frequent need for high-power evaluation. In addition, tumor grade is an integral part of the initial diagnosis. The purpose of this study is to assess the feasibility of primary pathology diagnosis of surgical neuropathology specimens using WSI. Materials and Methods: We reviewed consecutive surgical neuropathology cases diagnosed in our institution during a 2-month period and identified a single diagnostic slide, which was scanned at 40× magnification. Two neuropathologists who were blinded to the original diagnoses reviewed the whole slide image and rendered a diagnosis including tumor grade when applicable. They reviewed the single diagnostic slide after a wash-out period. Intra- and inter-observer discrepancies, as well as reasons for discrepancies, were evaluated. Results: The concordance rates were 94.9% and 88% for two neuropathologists. Two critical issues leading to discrepancies were identified: (1) identification of mitoses and (2) recognition of nuclear details. Conclusions: Given the current study is exclusively for surgical neuropathology cases, an all-encompassing conclusion about the utility of WSI for diagnostic purposes may not be available. Nevertheless, pathologists should be aware of the potential pitfalls due to identification of mitotic figures and nuclear details. We recommend independent validation for each subspecialty of pathology to identify subspecialty-specific concerns, so they can be properly addressed.
      Citation: Journal of Pathology Informatics 2016 7(1):25-25
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181769
      Issue No: Vol. 7, No. 1 (2016)
       
  • Evaluation of panoramic digital images using Panoptiq for frozen section
           diagnosis

    • Authors: Dinesh Pradhan, Sara E Monaco, Anil V Parwani, Ishtiaque Ahmed, Jon Duboy, Liron Pantanowitz
      Pages: 26 - 26
      Abstract: Dinesh Pradhan, Sara E Monaco, Anil V Parwani, Ishtiaque Ahmed, Jon Duboy, Liron Pantanowitz

      Journal of Pathology Informatics 2016 7(1):26-26

      Introduction: Whole slide imaging (WSI) permits intraoperative consultations (frozen sections) to be performed remotely. However, WSI files are large and can be problematic if there are tissue artifacts (e.g., tissue folds) or when slides are scanned without multiplanes (Z-stacks) to permit focusing. The Panoptiq dynamic imaging system allows users to create their own digital files that combine low power panoramic digital images with regions of interest that can be imaged using high power Z-stacks. The aim of this study was to determine the utility of the Panoptiq dynamic imaging system for frozen section telepathology. Materials and Methods: Twenty archival randomly selected genitourinary surgical pathology frozen sectional cases were evaluated using conventional light microscopy (glass slides), panoramic images, and whole slide images. To create panoramic images glass slides were digitized using a Prosilica GT camera (model GT1920C, Allied Vision Technologies) attached to an Olympus B × 45 microscope and Dell Precision Tower 810 computer (Dell). Panoptiq 3 version 3.1.2 software was used for image acquisition and Panoptiq View version 3.1.2 to view images (ViewsIQ, Richmond, BC, Canada). Image acquisition using Panoptiq software involved a pathology resident, who manually created digital maps (×4 objective) and then selected representative regions of interest to generate Z-stacks at higher magnification (×40 objective). Whole slide images were generated using an Aperio XT Scanscope (Leica) and viewed using ImageScope Software (Aperio ePathology, Leica). Three pathologists were asked to render diagnoses and rate image quality (1-10) and their diagnostic confidence (1-10) for each modality. Results: The diagnostic concordance with glass slides was 98.3% for panoramic images and 100% for WSI. Panoptiq images were comparable to the glass slide viewing experience in terms of image quality and diagnostic confidence. Complaints regarding WSI included poor focus near tissue folds and air bubbles. Panoptiq permitted fine focusing of tissue folds and air bubbles. Issues with panoramic images included difficulty interpreting low-resolution ×4 image maps and the presence of tiling artifacts. In some cases, Z-stacked areas of Panoptiq images were limited or not representative of diagnostic regions. The image file size of Panoptiq was more than 14 times smaller than that of WSI files. Conclusions: The Panoptiq imaging system is a novel tool that can be used for frozen section telepathology. Panoramic digital images were easy to generate and navigate, of relatively small file size, and offered a mechanism to overcome focusing problems commonly encountered with WSI of frozen sections. However, the acquisition of representative Panoptiq images was operator dependent with the individual creating files that may impact the final diagnosis.
      Citation: Journal of Pathology Informatics 2016 7(1):26-26
      PubDate: Wed,4 May 2016
      DOI: 10.4103/2153-3539.181770
      Issue No: Vol. 7, No. 1 (2016)
       
  • 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× (0.5 μm/pixel) and 40× (0.25 μm/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× 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 ±11 μm). The busulfan-treated animals showed marked heterogeneity in tubular size and shape (diameter 178 ± 35 μm) 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× and 40× 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, ≥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

    • 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

    • 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 ∆x was 4.00px (SD = 16.10), and ∆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® 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 ± 0.02 and a positive predictive value of 0.94 ± 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 β 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

    • 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

    • 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×, 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× 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 (~4-5μm thickness of a tissue section) is nearly the size of the objects of interest (~10-20μm 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 1μm) 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 5μm 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

    • 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

    • 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

    • 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× 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® 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
      DOI: 10.4103/2153-3539.82052
      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 (±0.27) μm 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; cervical cytology slides were scanned at three thickness settings: 18, 24, and 30 μm. 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˚C, 15 psi); 2) Ten dry autoclave cycles (121˚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˚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)
       
 
 
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