text:
Journal of Pathology Informatics
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Open Access journal
ISSN (Print) 2153-3539 - ISSN (Online) 2153-3539
Published by Medknow Publishers [304 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
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
Issue No: Vol. 7, No. 1 (2016)
- Oxygen supply maps for hypoxic microenvironment visualization in prostate
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
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
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
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
Issue No: Vol. 7, No. 1 (2016)
- Implementation of Epic Beaker Clinical Pathology at an academic medical
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
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
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
Issue No: Vol. 7, No. 1 (2016)
- Comparison of the diagnostic utility of digital pathology systems for
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
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
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
Issue No: Vol. 7, No. 1 (2016)
- Pathology interface for the molecular analysis of tissue by mass
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
Issue No: Vol. 7, No. 1 (2016)
- Perceptions of pathology informatics by non-informaticist pathologists and
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
Issue No: Vol. 7, No. 1 (2016)
- Quantitative analysis of myocardial tissue with digital autofluorescence
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
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
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
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
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
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
Issue No: Vol. 7, No. 1 (2016)
- Removing defocused objects from single focal plane scans of cytological
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
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
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
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
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
Issue No: Vol. 7, No. 1 (2016)
- Evaluation of panoramic digital images using Panoptiq for frozen section
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
Issue No: Vol. 7, No. 1 (2016)
- Virtual microscopy in the undergraduate teaching of pathology
Pages: 1 - 1
Abstract: Oriol Ordi, Josep Antoni Bombí, Antonio Martínez, Josep Ramírez, Llúcia Alòs, Adela Saco, Teresa Ribalta, Pedro L Fernández, Elias Campo, Jaume Ordi
Journal of Pathology Informatics 2015 6(1):1-1
Background: Little evidence is available concerning the impact of virtual microscopy (VM) in the undergraduate teaching of pathology. We aimed: (1) to determine the impact in student scores when moving from conventional microscopy (CM) to VM; (2) to assess the students' impressions and changes in study habits regarding the impact of this tool. Methods: We evaluated two groups taking the discipline of pathology in the same course, one using CM and the other VM. The same set of slides used in the CM classes was digitized in a VENTANA iScan HT (Roche Diagnostics, Sant Cugat, Spain) at ×20 and observed by the students using the Virtuoso viewer (Roche Diagnostics). We evaluated the skill level reached by the students with an online test. A voluntary survey was undertaken by the VM group to assess the students' impressions regarding the resource. The day and time of any accession to the viewer were registered. Results: There were no differences between the two groups in their marks in the online test (mean marks for the CM and the VM groups: 9.87 ± 0.34 and 9.86 ± 0.53, respectively; P = 0.880). 86.6% of the students found the software friendly, easy-to-use and effective. 71.6% of the students considered navigation easier with VM than with CM. The most appreciated feature of VM was the possibility to access the images anywhere and at any time (93.3%). 57.5% of the accesses were made on holidays and 41.9% later than 6:00 pm. Conclusions: Virtual microscopy can effectively replace the traditional methods of learning pathology, providing mobility and convenience to medical students.
Citation: Journal of Pathology Informatics 2015 6(1):1-1
PubDate: Thu,29 Jan 2015
Issue No: Vol. 6, No. 1 (2015)
- Development and validation of an app-based cell counter for use in the
clinical laboratory setting
Authors: Alexander C Thurman, Jessica L Davis, Max Jan, Charles E McCulloch, Benjamin D Buelow
Pages: 2 - 2
Abstract: Alexander C Thurman, Jessica L Davis, Max Jan, Charles E McCulloch, Benjamin D Buelow
Journal of Pathology Informatics 2015 6(1):2-2
Introduction: For decades cellular differentials have been generated exclusively on analog tabletop cell counters. With the advent of tablet computers, digital cell counters - in the form of mobile applications ("apps") - now represent an alternative to analog devices. However, app-based counters have not been widely adopted by clinical laboratories, perhaps owing to a presumed decrease in count accuracy related to the lack of tactile feedback inherent in a touchscreen interface. We herein provide the first systematic evidence that digital cell counters function similarly to standard tabletop units. Methods: We developed an app-based cell counter optimized for use in the clinical laboratory setting. Paired counts of 188 peripheral blood smears and 62 bone marrow aspirate smears were performed using our app-based counter and a standard analog device. Differences between paired data sets were analyzed using the correlation coefficient, Student's t-test for paired samples and Bland-Altman plots. Results: All counts showed excellent agreement across all users and touch screen devices. With the exception of peripheral blood basophils (r = 0.684), differentials generated for the measured cell categories within the paired data sets were highly correlated (all r ≥ 0.899). Results of paired t-tests did not reach statistical significance for any cell type (all P > 0.05), and Bland-Altman plots showed a narrow spread of the difference about the mean without evidence of significant outliers. Conclusions: Our analysis suggests that no systematic differences exist between cellular differentials obtained via app-based or tabletop counters and that agreement between these two methods is excellent.
Citation: Journal of Pathology Informatics 2015 6(1):2-2
PubDate: Thu,29 Jan 2015
Issue No: Vol. 6, No. 1 (2015)
- Reqscan: An open source solution for laboratory requisition scanning,
archiving and retrieval
Authors: Eviatar Bach, Daniel T Holmes
Pages: 3 - 3
Abstract: Eviatar Bach, Daniel T Holmes
Journal of Pathology Informatics 2015 6(1):3-3
Requisition storage and retrieval are an integral part of the outpatient laboratory testing process. It is frequently necessary to review an original requisition to confirm the ordering physician, patient demographics, diagnostic information, and requested tests. Manual retrieval of a paper requisition is time-consuming and tedious. Although commercial solutions exist for the scanning and archiving of barcoded paper requisitions, the tools to accomplish this are freely available from the open source software community. We present a simple dedicated piece of software, Reqscan, for scanning patient laboratory requisitions, finding all barcode information, and saving the requisition as a portable document format named according the barcode(s) found. This Python application offers a simple solution to patient requisition digitization. Reqscan has been successfully tested and implemented into routine practice for storage and retrieval of outpatient requisitions at St. Paul's Hospital, Department of Pathology and Laboratory Medicine in Vancouver, British Columbia, Canada.
Citation: Journal of Pathology Informatics 2015 6(1):3-3
PubDate: Thu,29 Jan 2015
Issue No: Vol. 6, No. 1 (2015)
- Evaluating whole slide imaging: A working group opportunity
Authors: Darren Treanor, Brandon D Gallas, Marios A Gavrielides, Stephen M Hewitt
Pages: 4 - 4
Abstract: Darren Treanor, Brandon D Gallas, Marios A Gavrielides, Stephen M Hewitt
Journal of Pathology Informatics 2015 6(1):4-4
Citation: Journal of Pathology Informatics 2015 6(1):4-4
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- Summary of 2 nd Nordic symposium on digital pathology
Pages: 5 - 5
Abstract: Claes Lundström, Sten Thorstenson, Marie Waltersson, Anders Persson, Darren Treanor
Journal of Pathology Informatics 2015 6(1):5-5
Techniques for digital pathology are envisioned to provide great benefits in clinical practice, but experiences also show that solutions must be carefully crafted. The Nordic countries are far along the path toward the use of whole-slide imaging in clinical routine. The Nordic Symposium on Digital Pathology (NDP) was created to promote knowledge exchange in this area, between stakeholders in health care, industry, and academia. This article is a summary of the NDP 2014 symposium, including conclusions from a workshop on clinical adoption of digital pathology among the 144 attendees.
Citation: Journal of Pathology Informatics 2015 6(1):5-5
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- Histopathology in 3D: From three-dimensional reconstruction to multi-stain
and multi-modal analysis
Authors: Derek Magee, Yi Song, Stephen Gilbert, Nicholas Roberts, Nagitha Wijayathunga, Ruth Wilcox, Andrew Bulpitt, Darren Treanor
Pages: 6 - 6
Abstract: Derek Magee, Yi Song, Stephen Gilbert, Nicholas Roberts, Nagitha Wijayathunga, Ruth Wilcox, Andrew Bulpitt, Darren Treanor
Journal of Pathology Informatics 2015 6(1):6-6
Light microscopy applied to the domain of histopathology has traditionally been a two-dimensional imaging modality. Several authors, including the authors of this work, have extended the use of digital microscopy to three dimensions by stacking digital images of serial sections using image-based registration. In this paper, we give an overview of our approach, and of extensions to the approach to register multi-modal data sets such as sets of interleaved histopathology sections with different stains, and sets of histopathology images to radiology volumes with very different appearance. Our approach involves transforming dissimilar images into a multi-channel representation derived from co-occurrence statistics between roughly aligned images.
Citation: Journal of Pathology Informatics 2015 6(1):6-6
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- A comparative study of input devices for digital slide navigation
Pages: 7 - 7
Abstract: Jesper Molin, Claes Lundström, Morten Fjeld
Journal of Pathology Informatics 2015 6(1):7-7
This paper describes work presented at the Nordic Symposium on Digital Pathology 2014, Linköping, Sweden. Quick and seamless integration between input devices and the navigation of digital slides remains a key barrier for many pathologists to "go digital." To better understand this integration, three different input device implementations were compared in terms of time to diagnose, perceived workload and users' preferences. Six pathologists reviewed in total nine cases with a computer mouse, a 6 degrees-of-freedom (6DOF) navigator and a touchpad. The participants perceived significantly less workload (P < 0.05) with the computer mouse and the 6DOF navigator, than with the touchpad, while no effect of the input device used on the time to diagnose was observed. Five out of six pathologists preferred the 6DOF navigator, while the touchpad was the least preferred device. While digital slide navigation is often designed to mimic microscope interaction, the results of this study demonstrate that in order to minimize workload there is reason to let the digital interaction move beyond the familiar microscope tradition.
Citation: Journal of Pathology Informatics 2015 6(1):7-7
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- RandomSpot: A web-based tool for systematic random sampling of virtual
Authors: Alexander I Wright, Heike I Grabsch, Darren E Treanor
Pages: 8 - 8
Abstract: Alexander I Wright, Heike I Grabsch, Darren E Treanor
Journal of Pathology Informatics 2015 6(1):8-8
This paper describes work presented at the Nordic Symposium on Digital Pathology 2014, Linköping, Sweden. Systematic random sampling (SRS) is a stereological tool, which provides a framework to quickly build an accurate estimation of the distribution of objects or classes within an image, whilst minimizing the number of observations required. RandomSpot is a web-based tool for SRS in stereology, which systematically places equidistant points within a given region of interest on a virtual slide. Each point can then be visually inspected by a pathologist in order to generate an unbiased sample of the distribution of classes within the tissue. Further measurements can then be derived from the distribution, such as the ratio of tumor to stroma. RandomSpot replicates the fundamental principle of traditional light microscope grid-shaped graticules, with the added benefits associated with virtual slides, such as facilitated collaboration and automated navigation between points. Once the sample points have been added to the region(s) of interest, users can download the annotations and view them locally using their virtual slide viewing software. Since its introduction, RandomSpot has been used extensively for international collaborative projects, clinical trials and independent research projects. So far, the system has been used to generate over 21,000 sample sets, and has been used to generate data for use in multiple publications, identifying significant new prognostic markers in colorectal, upper gastro-intestinal and breast cancer. Data generated using RandomSpot also has significant value for training image analysis algorithms using sample point coordinates and pathologist classifications.
Citation: Journal of Pathology Informatics 2015 6(1):8-8
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- Clinical laboratory analytics: Challenges and promise for an emerging
Authors: Brian H Shirts, Brian R Jackson, Geoffrey S Baird, Jason M Baron, Bryan Clements, Ricky Grisson, Ronald George Hauser, Julie R Taylor, Enrique Terrazas, Brad Brimhall
Pages: 9 - 9
Abstract: Brian H Shirts, Brian R Jackson, Geoffrey S Baird, Jason M Baron, Bryan Clements, Ricky Grisson, Ronald George Hauser, Julie R Taylor, Enrique Terrazas, Brad Brimhall
Journal of Pathology Informatics 2015 6(1):9-9
The clinical laboratory is a major source of health care data. Increasingly these data are being integrated with other data to inform health system-wide actions meant to improve diagnostic test utilization, service efficiency, and "meaningful use." The Academy of Clinical Laboratory Physicians and Scientists hosted a satellite meeting on clinical laboratory analytics in conjunction with their annual meeting on May 29, 2014 in San Francisco. There were 80 registrants for the clinical laboratory analytics meeting. The meeting featured short presentations on current trends in clinical laboratory analytics and several panel discussions on data science in laboratory medicine, laboratory data and its role in the larger healthcare system, integrating laboratory analytics, and data sharing for collaborative analytics. One main goal of meeting was to have an open forum of leaders that work with the "big data" clinical laboratories produce. This article summarizes the proceedings of the meeting and content discussed.
Citation: Journal of Pathology Informatics 2015 6(1):9-9
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- A bayesian approach to laboratory utilization management
Authors: Ronald G Hauser, Brian R Jackson, Brian H Shirts
Pages: 10 - 10
Abstract: Ronald G Hauser, Brian R Jackson, Brian H Shirts
Journal of Pathology Informatics 2015 6(1):10-10
Background: Laboratory utilization management describes a process designed to increase healthcare value by altering requests for laboratory services. A typical approach to monitor and prioritize interventions involves audits of laboratory orders against specific criteria, defined as rule-based laboratory utilization management. This approach has inherent limitations. First, rules are inflexible. They adapt poorly to the ambiguity of medical decision-making. Second, rules judge the context of a decision instead of the patient outcome allowing an order to simultaneously save a life and break a rule. Third, rules can threaten physician autonomy when used in a performance evaluation. Methods: We developed an alternative to rule-based laboratory utilization. The core idea comes from a formula used in epidemiology to estimate disease prevalence. The equation relates four terms: the prevalence of disease, the proportion of positive tests, test sensitivity and test specificity. When applied to a laboratory utilization audit, the formula estimates the prevalence of disease (pretest probability [PTP]) in the patients tested. The comparison of PTPs among different providers, provider groups, or patient cohorts produces an objective evaluation of laboratory requests. We demonstrate the model in a review of tests for enterovirus (EV) meningitis. Results: The model identified subpopulations within the cohort with a low prevalence of disease. These low prevalence groups shared demographic and seasonal factors known to protect against EV meningitis. This suggests too many orders occurred from patients at low risk for EV. Conclusion: We introduce a new method for laboratory utilization management programs to audit laboratory services.
Citation: Journal of Pathology Informatics 2015 6(1):10-10
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- Performance of the CellaVision ® DM96 system for detecting red
blood cell morphologic abnormalities
Authors: Christopher L Horn, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Lik Hang Lee, Christopher Naugler
Pages: 11 - 11
Abstract: Christopher L Horn, Adnan Mansoor, Brenda Wood, Heather Nelson, Diane Higa, Lik Hang Lee, Christopher Naugler
Journal of Pathology Informatics 2015 6(1):11-11
Background: Red blood cell (RBC) analysis is a key feature in the evaluation of hematological disorders. The gold standard light microscopy technique has high sensitivity, but is a relativity time-consuming and labor intensive procedure. This study tested the sensitivity and specificity of gold standard light microscopy manual differential to the CellaVision ® DM96 (CCS; CellaVision, Lund, Sweden) automated image analysis system, which takes digital images of samples at high magnification and compares these images with an artificial neural network based on a database of cells and preclassified according to RBC morphology. Methods: In this study, 212 abnormal peripheral blood smears within the Calgary Laboratory Services network of hospital laboratories were selected and assessed for 15 different RBC morphologic abnormalities by manual microscopy. The same samples were reassessed as a manual addition from the instrument screen using the CellaVision ® DM96 system with 8 microscope high power fields (×100 objective and a 22 mm ocular). The results of the investigation were then used to calculate the sensitivity and specificity of the CellaVision ® DM96 system in reference to light microscopy. Results: The sensitivity ranged from a low of 33% (RBC agglutination) to a high of 100% (sickle cells, stomatocytes). The remainder of the RBC abnormalities tested somewhere between these two extremes. The specificity ranged from 84% (schistocytes) to 99.5% (sickle cells, stomatocytes). Conclusions: Our results showed generally high specificities but variable sensitivities for RBC morphologic abnormalities.
Citation: Journal of Pathology Informatics 2015 6(1):11-11
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- Review of "digital pathology" by Yves Sucaet and Wim Waelput
Authors: John H Sinard
Pages: 12 - 12
Abstract: John H Sinard
Journal of Pathology Informatics 2015 6(1):12-12
Citation: Journal of Pathology Informatics 2015 6(1):12-12
PubDate: Tue,24 Feb 2015
Issue No: Vol. 6, No. 1 (2015)
- 2014 American Telemedicine Association clinical guidelines for
telepathology: Another important step in support of increased adoption of
telepathology for patient care
Authors: Andrew J Evans, Elizabeth A Krupinski, Ronald S Weinstein, Liron Pantanowitz
Pages: 13 - 13
Abstract: Andrew J Evans, Elizabeth A Krupinski, Ronald S Weinstein, Liron Pantanowitz
Journal of Pathology Informatics 2015 6(1):13-13
Citation: Journal of Pathology Informatics 2015 6(1):13-13
PubDate: Tue,24 Mar 2015
Issue No: Vol. 6, No. 1 (2015)
- Telecytopathology facilitates the use of rapid on-site evaluation in
endoscopic ultraound fine needle aspiration of the pancreas to improve
patient outcomes
Authors: Brian T Collins
Pages: 14 - 14
Abstract: Brian T Collins
Journal of Pathology Informatics 2015 6(1):14-14
Citation: Journal of Pathology Informatics 2015 6(1):14-14
PubDate: Tue,24 Mar 2015
Issue No: Vol. 6, No. 1 (2015)
- Automated discrimination of lower and higher grade gliomas based on
histopathological image analysis
Authors: Hojjat Seyed Mousavi, Vishal Monga, Ganesh Rao, Arvind U. K. Rao
Pages: 15 - 15
Abstract: Hojjat Seyed Mousavi, Vishal Monga, Ganesh Rao, Arvind U. K. Rao
Journal of Pathology Informatics 2015 6(1):15-15
Introduction: Histopathological images have rich structural information, are multi-channel in nature and contain meaningful pathological information at various scales. Sophisticated image analysis tools that can automatically extract discriminative information from the histopathology image slides for diagnosis remain an area of significant research activity. In this work, we focus on automated brain cancer grading, specifically glioma grading. Grading of a glioma is a highly important problem in pathology and is largely done manually by medical experts based on an examination of pathology slides (images). To complement the efforts of clinicians engaged in brain cancer diagnosis, we develop novel image processing algorithms and systems to automatically grade glioma tumor into two categories: Low-grade glioma (LGG) and high-grade glioma (HGG) which represent a more advanced stage of the disease. Results: We propose novel image processing algorithms based on spatial domain analysis for glioma tumor grading that will complement the clinical interpretation of the tissue. The image processing techniques are developed in close collaboration with medical experts to mimic the visual cues that a clinician looks for in judging of the grade of the disease. Specifically, two algorithmic techniques are developed: (1) A cell segmentation and cell-count profile creation for identification of Pseudopalisading Necrosis, and (2) a customized operation of spatial and morphological filters to accurately identify microvascular proliferation (MVP). In both techniques, a hierarchical decision is made via a decision tree mechanism. If either Pseudopalisading Necrosis or MVP is found present in any part of the histopathology slide, the whole slide is identified as HGG, which is consistent with World Health Organization guidelines. Experimental results on the Cancer Genome Atlas database are presented in the form of: (1) Successful detection rates of pseudopalisading necrosis and MVP regions, (2) overall classification accuracy into LGG and HGG categories, and (3) receiver operating characteristic curves which can facilitate a desirable trade-off between HGG detection and false-alarm rates. Conclusion: The proposed method demonstrates fairly high accuracy and compares favorably against best-known alternatives such as the state-of-the-art WND-CHARM feature set provided by NIH combined with powerful support vector machine classifier. Our results reveal that the proposed method can be beneficial to a clinician in effectively separating histopathology slides into LGG and HGG categories, particularly where the analysis of a large number of slides is needed. Our work also reveals that MVP regions are much harder to detect than Pseudopalisading Necrosis and increasing accuracy of automated image processing for MVP detection emerges as a significant future research direction.
Citation: Journal of Pathology Informatics 2015 6(1):15-15
PubDate: Tue,24 Mar 2015
Issue No: Vol. 6, No. 1 (2015)
- Default settings of computerized physician order entry system order sets
drive ordering habits
Authors: Jordan Olson, Christopher Hollenbeak, Keri Donaldson, Thomas Abendroth, William Castellani
Pages: 16 - 16
Abstract: Jordan Olson, Christopher Hollenbeak, Keri Donaldson, Thomas Abendroth, William Castellani
Journal of Pathology Informatics 2015 6(1):16-16
Background: Computerized physician order entry (CPOE) systems are quickly becoming ubiquitous, and groups of orders ("order sets") to allow for easy order input are a common feature. This provides a streamlined mechanism to view, modify, and place groups of related orders. This often serves as an electronic equivalent of a specialty requisition. A characteristic, of these order sets is that specific orders can be predetermined to be "preselected" or "defaulted-on" whenever the order set is used while others are "optional" or "defaulted-off" (though there is typically the option is to "deselect" defaulted-on tests in a given situation). While it seems intuitive that the defaults in an order set are often accepted, additional study is required to understand the impact of these "default" settings in an order set on ordering habits. This study set out to quantify the effect of changing the default settings of an order set. Methods: For quality improvement purposes, order sets dealing with transfusions were recently reviewed and modified to improve monitoring of outcome. Initially, the order for posttransfusion hematocrits and platelet count had the default setting changed from "optional" to "preselected." The default settings for platelet count was later changed back to "optional," allowing for a natural experiment to study the effect of the default selections of an order set on clinician ordering habits. Results: Posttransfusion hematocrit values were ordered for 8.3% of red cell transfusions when the default order set selection was "off" and for 57.4% of transfusions when the default selection was "preselected" (P < 0.0001). Posttransfusion platelet counts were ordered for 7.0% of platelet transfusions when the initial default order set selection was "optional," increased to 59.4% when the default was changed to "preselected" (P < 0.0001), and then decreased to 7.5% when the default selection was returned to "optional." The posttransfusion platelet count rates during the two "optional" periods: 7.0% versus 7.5% - were not statistically different (P = 0.620). Discussion: Default settings in CPOE order sets can significantly influence physician selection of laboratory tests. Careful consideration by all stakeholders, including clinicians and pathologists, should be obtained when establishing default settings in order sets.
Citation: Journal of Pathology Informatics 2015 6(1):16-16
PubDate: Tue,24 Mar 2015
Issue No: Vol. 6, No. 1 (2015)
- Imaging file management to support international telepathology
Authors: Liron Pantanowitz, Jeffrey McHugh, William Cable, Chengquan Zhao, Anil V Parwani
Pages: 17 - 17
Abstract: Liron Pantanowitz, Jeffrey McHugh, William Cable, Chengquan Zhao, Anil V Parwani
Journal of Pathology Informatics 2015 6(1):17-17
Background: Telepathology practice across international borders has become increasingly popular. Our telepathology consultation service with a laboratory in China was hampered by latency issues when viewing whole slide images. Objective: The aim was to explore data transfer solutions to improve the viewing experience of digital consult cases. Methods: Whole slide image files residing on a server in China were transferred to our data center in the USA using an open source product (Fast Data Transfer). A faster more automated commercial high speed file transfer software solution (Aspera) was also tested. Results: Transferring files with the open source product provided transfer speeds of 2-3 Mbps, but suffered from intermittent dropped connections. Employing commercial software permitted more reliable transmission of digital files with 75-100 Mbps transfer speeds. Conclusions: Successful global telepathology requires dedicated image management. Transfer of files to local servers by employing high speed data transfer tools helped overcome network latency issues, improved the overall turn-around time of digital consultations, and enhanced the viewing experience for end-user digital consultants.
Citation: Journal of Pathology Informatics 2015 6(1):17-17
PubDate: Tue,24 Mar 2015
Issue No: Vol. 6, No. 1 (2015)
- Distance reporting in digital pathology: A study on 950 cases
Authors: Aleksandar Vodovnik
Pages: 18 - 18
Abstract: Aleksandar Vodovnik
Journal of Pathology Informatics 2015 6(1):18-18
Background: Increased workload, case complexity, financial constraints, and staffing shortages justify wider implementations of digital pathology. One of its main advantages is distance reporting. Aim: A feasibility study was conducted at our institution in order to achieve comprehensive pathology services available by distance. Methods: One senior pathologist reported 950 cases (3,650 slides) by distance during 19 weeks. Slides were scanned by ScanScope AT Turbo (Aperio) and digital images accessed through SymPathy (Tieto) on a 14" laptop. Mobile phone, mobile broadband, broadband over Wi-Fi and broadband were used for internet connections along with a virtual private network technology (VPN). Lync (Microsoft) was tested for one case consultation and resident's teaching session. Larger displays were accessed when available. Effects of ergonomics and working flexibility on the user experience were observed. Details on network speed, frequency of technical issues, data usage, scanning, and turnaround, were collected and evaluated. Turnaround was compared to in-office microscopic reporting, measured from the registration to sign off. Results: Network speeds varied 1-80 Mbps (median download speed 8-65 Mbps). 20 Mbps were satisfactory for the instant upload of digital images. VPN, image viewer, and laptop failed on two occasions each. An estimated data usage per digital image was 10 MB (1-50 MB). Two cases (15 slides) were deferred to microscopic slides (0.21/0.41%) due to scanty material and suboptimal slide quality. Additional nine cases (15 slides) needed to be rescanned for various reasons (0.95/0.41%). Average turnaround was shorter, and the percentage of cases reported up to 3 days higher (3.13 days/72.25%) comparing with in-office microscopic reporting (3.90 days/40.56%). Larger displays improved the most user experience at magnifications over Χ20. Conclusions: Existing IT solutions at our institution allow efficient and reliable distance reporting for the core pathology services in histology and cytology. Stable network speeds, fully integrated laboratory information management system, technical reliability, working flexibility, larger displays, and shorter turnaround contributed to the overall satisfaction with distance reporting. A further expansion of our pathology services available by distance, diagnostic and educational, rely on gaining experience in digital reporting and marginal IT investment. Adjustments to the organization of pathology services may follow to fully benefit from the implementation of digital pathology.
Citation: Journal of Pathology Informatics 2015 6(1):18-18
PubDate: Thu,30 Apr 2015
Issue No: Vol. 6, No. 1 (2015)
- Rapid on-site evaluation with dynamic telecytopathology for
ultrasound-guided fine-needle aspiration of head and neck nonthyroid
Authors: Kamal K Khurana, Weisheng Xu, Dongliang Wang, Amar Swarnkar
Pages: 19 - 19
Abstract: Kamal K Khurana, Weisheng Xu, Dongliang Wang, Amar Swarnkar
Journal of Pathology Informatics 2015 6(1):19-19
Background: Rapid on-site evaluation (ROSE) at the time of ultrasound-guided fine-needle aspiration (USGFNA) of head and neck lesion is essential for obtaining adequate samples and providing the preliminary diagnosis. We summarize our experience with ROSE of USGFNA on head and neck nonthyroid lesions using telecytopathology. Materials and Methods: Real-time images of Diff-Quik stained cytology smears were obtained at ultrasound suite with an Olympus DP-70 digital camera attached to an Olympus CX41 microscope, and transmitted via ethernet by a cytotechnologist to a cytopathologist in cytopathology laboratory who rendered a preliminary diagnosis. Live communication was conducted with Vocera voice communication system. The ultrasound suite was located on different floor from the cytopathology laboratory. Accuracy of ROSE via telecytopathology was compared with an equal number of cases that received ROSE, prior to introduction of telecytopathology, via conventional microscopy. Results: Rapid on-site evaluation was performed on a total of 116 USGFNA of head and neck nonthyroid lesions. The telecytopathology system and conventional microscopy was used to evaluate equal number of cases (58 each). Preliminary diagnoses of benign, atypical/suspicious for malignancy, and positive for malignancy were 72.4%, 17.2% and 10.3% for telecytopathology, and 69.0%, 10.3% and 20.7% for conventional microscopy. None of the cases were deemed unsatisfactory. The overall concordance between the preliminary and final diagnoses was 94.8% for telecytopathology and 98.3% for conventional microscopy and was not statistically significant (P = 0.309). The causes of discordant preliminary and final diagnoses were mainly attributed to availability of cell block and Papanicolaou-stained slides for review or flow cytometry results for lymphoma cases at the time of final sign out. Conclusions: Telecytopathology is comparable with conventional microscopy in ROSE of USGFNA of head and neck nonthyroid lesions.
Citation: Journal of Pathology Informatics 2015 6(1):19-19
PubDate: Thu,28 May 2015
Issue No: Vol. 6, No. 1 (2015)
- Automated morphometry provides accurate and reproducible virtual staging
of liver fibrosis in chronic hepatitis C
Pages: 20 - 20
Abstract: Paul Calès, Julien Chaigneau, Gilles Hunault, Sophie Michalak, Christine Cavaro-Menard, Jean-Baptiste Fasquel, Sandrine Bertrais, Marie-Christine Rousselet
Journal of Pathology Informatics 2015 6(1):20-20
Background: Liver fibrosis staging provides prognostic value, although hampered by observer variability. We used digital analysis to develop diagnostic morphometric scores for significant fibrosis, cirrhosis and fibrosis staging in chronic hepatitis C. Materials and Methods: We automated the measurement of 44 classical and new morphometric descriptors. The reference was histological METAVIR fibrosis (F) staging (F0 to F4) on liver biopsies. The derivation population included 416 patients and liver biopsies ≥20 mm-length. Two validation population included 438 patients. Results: In the derivation population, the area under the receiver operating characteristic (AUROC) for clinically significant fibrosis (F stage ≥2) of a logistic score combining 5 new descriptors (stellar fibrosis area, edge linearity, bridge thickness, bridge number, nodularity) was 0.957. The AUROC for cirrhosis of 6 new descriptors (edge linearity, nodularity, portal stellar fibrosis area, portal distance, granularity, fragmentation) was 0.994. Predicted METAVIR F staging combining 8 morphometric descriptors agreed well with METAVIR F staging by pathologists: k = 0.868. Morphometric score of clinically significant fibrosis had a higher correlation with porto-septal fibrosis area (rs = 0.835) than METAVIR F staging (rs = 0.756, P < 0.001) and the same correlations with fibrosis biomarkers, e.g., serum hyaluronate: rs = 0.484 versus rs = 0.476 for METAVIR F (P = 0.862). In the validation population, the AUROCs of clinically significant fibrosis and cirrhosis scores were, respectively: 0.893 and 0.993 in 153 patients (biopsy < 20 mm); 0.955 and 0.994 in 285 patients (biopsy ≥ 20 mm). The three morphometric diagnoses agreed with consensus expert reference as well as or better than diagnoses by first-line pathologists in 285 patients, respectively: significant fibrosis: 0.733 versus 0.733 (k), cirrhosis: 0.900 versus 0.827, METAVIR F: 0.881 versus 0.865. Conclusion: The new automated morphometric scores provide reproducible and accurate diagnoses of fibrosis stages via "virtual expert pathologist."
Citation: Journal of Pathology Informatics 2015 6(1):20-20
PubDate: Thu,28 May 2015
Issue No: Vol. 6, No. 1 (2015)
- Prospector: A web-based tool for rapid acquisition of gold standard data
for pathology research and image analysis
Authors: Alexander I Wright, Derek R Magee, Philip Quirke, Darren E Treanor
Pages: 21 - 21
Abstract: Alexander I Wright, Derek R Magee, Philip Quirke, Darren E Treanor
Journal of Pathology Informatics 2015 6(1):21-21
Background: Obtaining ground truth for pathological images is essential for various experiments, especially for training and testing image analysis algorithms. However, obtaining pathologist input is often difficult, time consuming and expensive. This leads to algorithms being over-fitted to small datasets, and inappropriate validation, which causes poor performance on real world data. There is a great need to gather data from pathologists in a simple and efficient manner, in order to maximise the amount of data obtained. Methods: We present a lightweight, web-based HTML5 system for administering and participating in data collection experiments. The system is designed for rapid input with minimal effort, and can be accessed from anywhere in the world with a reliable internet connection. Results: We present two case studies that use the system to assess how limitations on fields of view affect pathologist agreement, and to what extent poorly stained slides affect judgement. In both cases, the system collects pathologist scores at a rate of less than two seconds per image. Conclusions: The system has multiple potential applications in pathology and other domains.
Citation: Journal of Pathology Informatics 2015 6(1):21-21
PubDate: Thu,28 May 2015
Issue No: Vol. 6, No. 1 (2015)
- Whole slide imaging for human epidermal growth factor receptor 2
immunohistochemistry interpretation: Accuracy, Precision, and
reproducibility studies for digital manual and paired glass slide manual
Authors: David C Wilbur, Elena F Brachtel, John R Gilbertson, Nicholas C Jones, John G Vallone, Savitra Krishnamurthy
Pages: 22 - 22
Abstract: David C Wilbur, Elena F Brachtel, John R Gilbertson, Nicholas C Jones, John G Vallone, Savitra Krishnamurthy
Journal of Pathology Informatics 2015 6(1):22-22
Background: The use of digital whole slide imaging for human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) could create improvements in workflow and performance, allowing for central archiving of specimens, distributed and remote interpretation, and the potential for additional computerized automation. Procedures: The accuracy, precision, and reproducibility of manual digital interpretation for HER2 IHC were determined by comparison to manual glass slide interpretation. Inter- and intra-pathologist reproducibility and precision between the glass slide and digital interpretations of HER2 IHC were determined in 5 studies using DAKO HercepTest-stained breast cancer slides with the Philips Digital Pathology System. In 2 inter-method studies, 3 pathologists interpreted glass and digital slides in sequence or in random order with a minimum of 7 days as a washout period. These studies also measured inter-observer reproducibility and precision. Another two studies measured intra-pathologist reproducibility on cases read 10 times by glass and digital methods. One additional study evaluated the effects of adding IHC control slides with each run, using 1 pathologist interpreting glass and digital slides randomized from the sets above along with appropriate controls for each slide in the set. Results: The overall results show that there is no statistical difference between the variance of performance when comparing glass and digital HER2 interpretations; and there were no effects noted when control tissues were evaluated in conjunction with the test slides. Conclusions: The results show that there is an equivalence of result when interpreting HER2 IHC slides in breast cancer by either glass slides or digital images. Digital interpretation can therefore be safely and effectively used for this purpose.
Citation: Journal of Pathology Informatics 2015 6(1):22-22
PubDate: Thu,28 May 2015
Issue No: Vol. 6, No. 1 (2015)
- A review of the current state of digital plate reading of cultures in
clinical microbiology
Authors: Daniel D Rhoads, Susan M Novak, Liron Pantanowitz
Pages: 23 - 23
Abstract: Daniel D Rhoads, Susan M Novak, Liron Pantanowitz
Journal of Pathology Informatics 2015 6(1):23-23
Digital plate reading (DPR) is increasingly being adopted as a means to facilitate the analysis and improve the quality and efficiency within the clinical microbiology laboratory. This review discusses the role of DPR in the context of total laboratory automation and explores some of the platforms currently available or in development for digital image capturing of microbial growth on media. The review focuses on the advantages and challenges of DPR. Peer-reviewed studies describing the utility and quality of these novel DPR systems are largely lacking, and professional guidelines for DPR implementation and quality management are needed. Further development and more widespread adoption of DPR is anticipated.
Citation: Journal of Pathology Informatics 2015 6(1):23-23
PubDate: Thu,28 May 2015
Issue No: Vol. 6, No. 1 (2015)
- Abstracts: Pathology Informatics 2015
Pages: 24 - 24
Journal of Pathology Informatics 2015 6(1):24-24
Citation: Journal of Pathology Informatics 2015 6(1):24-24
PubDate: Tue,2 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Reimagining the microscope in the 21 st century using the scalable
adaptive graphics environment
Authors: Victor Mateevitsi, Tushar Patel, Jason Leigh, Bruce Levy
Pages: 25 - 25
Abstract: Victor Mateevitsi, Tushar Patel, Jason Leigh, Bruce Levy
Journal of Pathology Informatics 2015 6(1):25-25
Background: Whole-slide imaging (WSI), while technologically mature, remains in the early adopter phase of the technology adoption lifecycle. One reason for this current situation is that current methods of visualizing and using WSI closely follow long-existing workflows for glass slides. We set out to "reimagine" the digital microscope in the era of cloud computing by combining WSI with the rich collaborative environment of the Scalable Adaptive Graphics Environment (SAGE). SAGE is a cross-platform, open-source visualization and collaboration tool that enables users to access, display and share a variety of data-intensive information, in a variety of resolutions and formats, from multiple sources, on display walls of arbitrary size. Methods: A prototype of a WSI viewer app in the SAGE environment was created. While not full featured, it enabled the testing of our hypothesis that these technologies could be blended together to change the essential nature of how microscopic images are utilized for patient care, medical education, and research. Results: Using the newly created WSI viewer app, demonstration scenarios were created in the patient care and medical education scenarios. This included a live demonstration of a pathology consultation at the International Academy of Digital Pathology meeting in Boston in November 2014. Conclusions: SAGE is well suited to display, manipulate and collaborate using WSIs, along with other images and data, for a variety of purposes. It goes beyond how glass slides and current WSI viewers are being used today, changing the nature of digital pathology in the process. A fully developed WSI viewer app within SAGE has the potential to encourage the wider adoption of WSI throughout pathology.
Citation: Journal of Pathology Informatics 2015 6(1):25-25
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Enhancing automatic classification of hepatocellular carcinoma images
through image masking, tissue changes and trabecular features
Authors: Maulana Abdul Aziz, Hiroshi Kanazawa, Yuri Murakami, Fumikazu Kimura, Masahiro Yamaguchi, Tomoharu Kiyuna, Yoshiko Yamashita, Akira Saito, Masahiro Ishikawa, Naoki Kobayashi, Tokiya Abe, Akinori Hashiguchi, Michiie Sakamoto
Pages: 26 - 26
Abstract: Maulana Abdul Aziz, Hiroshi Kanazawa, Yuri Murakami, Fumikazu Kimura, Masahiro Yamaguchi, Tomoharu Kiyuna, Yoshiko Yamashita, Akira Saito, Masahiro Ishikawa, Naoki Kobayashi, Tokiya Abe, Akinori Hashiguchi, Michiie Sakamoto
Journal of Pathology Informatics 2015 6(1):26-26
Background: Recent breakthroughs in computer vision and digital microscopy have prompted the application of such technologies in cancer diagnosis, especially in histopathological image analysis. Earlier, an attempt to classify hepatocellular carcinoma images based on nuclear and structural features has been carried out on a set of surgical resected samples. Here, we proposed methods to enhance the process and improve the classification performance. Methods: First, we segmented the histological components of the liver tissues and generated several masked images. By utilizing the masked images, some set of new features were introduced, producing three sets of features consisting nuclei, trabecular and tissue changes features. Furthermore, we extended the classification process by using biopsy resected samples in addition to the surgical samples. Results: Experiments by using support vector machine (SVM) classifier with combinations of features and sample types showed that the proposed methods improve the classification rate in HCC detection for about 1-3%. Moreover, detection rate of low-grades cancer increased when the new features were appended in the classification process, although the rate was worsen in the case of undifferentiated tumors. Conclusions: The masking process increased the reliability of extracted nuclei features. The additional of new features improved the system especially for early HCC detection. Likewise, the combination of surgical and biopsy samples as training data could also improve the classification rates. Therefore, the methods will extend the support for pathologists in the HCC diagnosis.
Citation: Journal of Pathology Informatics 2015 6(1):26-26
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Understanding the three-dimensional world from two-dimensional
immunofluorescent adjacent sections
Authors: Sho Fujisawa, Dmitry Yarilin, Ning Fan, Mesruh Turkekul, Ke Xu, Afsar Barlas, Katia Manova-Todorova
Pages: 27 - 27
Abstract: Sho Fujisawa, Dmitry Yarilin, Ning Fan, Mesruh Turkekul, Ke Xu, Afsar Barlas, Katia Manova-Todorova
Journal of Pathology Informatics 2015 6(1):27-27
Visualizing tissue structures in three-dimensions (3D) is crucial to understanding normal and pathological phenomena. However, staining and imaging of thick sections and whole mount samples can be challenging. For decades, researchers have serially sectioned large tissues and painstakingly reconstructed the 3D volume. Advances in automation, from sectioning to alignment, now greatly accelerate the process. In addition, immunofluorescent staining methods allow multiple antigens to be simultaneously detected and analyzed volumetrically. The objective was to incorporate multi-channel immunofluorescent staining and automation in 3D reconstruction of serial sections for volumetric analysis. Paraffin-embedded samples were sectioned manually but were processed, stained, imaged and aligned in an automated fashion. Reconstructed stacks were quantitatively analyzed in 3D. By combining automated immunofluorescent staining and tried-and-true methods of reconstructing adjacent sections, we were able to visualize, in detail, not only the geometric structures of the sample but also the presence and interactions of multiple proteins and molecules of interest within their 3D environment. Advances in technology and software algorithms have significantly expedited the 3D reconstruction of serial sections. Automated, multi-antigen immunofluorescent staining will significantly broaden the range and complexity of scientific questions that can be answered with this methodology.
Citation: Journal of Pathology Informatics 2015 6(1):27-27
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Exploring viewing behavior data from whole slide images to predict
correctness of students' answers during practical exams in oral
Authors: Slawomir Walkowski, Mikael Lundin, Janusz Szymas, Johan Lundin
Pages: 28 - 28
Abstract: Slawomir Walkowski, Mikael Lundin, Janusz Szymas, Johan Lundin
Journal of Pathology Informatics 2015 6(1):28-28
The way of viewing whole slide images (WSI) can be tracked and analyzed. In particular, it can be useful to learn how medical students view WSIs during exams and how their viewing behavior is correlated with correctness of the answers they give. We used software-based view path tracking method that enabled gathering data about viewing behavior of multiple simultaneous WSI users. This approach was implemented and applied during two practical exams in oral pathology in 2012 (88 students) and 2013 (91 students), which were based on questions with attached WSIs. Gathered data were visualized and analyzed in multiple ways. As a part of extended analysis, we tried to use machine learning approaches to predict correctness of students' answers based on how they viewed WSIs. We compared the results of analyses for years 2012 and 2013 - done for a single question, for student groups, and for a set of questions. The overall patterns were generally consistent across these 3 years. Moreover, viewing behavior data appeared to have certain potential for predicting answers' correctness and some outcomes of machine learning approaches were in the right direction. However, general prediction results were not satisfactory in terms of precision and recall. Our work confirmed that the view path tracking method is useful for discovering viewing behavior of students analyzing WSIs. It provided multiple useful insights in this area, and general results of our analyses were consistent across two exams. On the other hand, predicting answers' correctness appeared to be a difficult task - students' answers seem to be often unpredictable.
Citation: Journal of Pathology Informatics 2015 6(1):28-28
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- A perspective on digital and computational pathology
Authors: Bhagavathi Ramamurthy, Frederick D Coffman, Stanley Cohen
Pages: 29 - 29
Abstract: Bhagavathi Ramamurthy, Frederick D Coffman, Stanley Cohen
Journal of Pathology Informatics 2015 6(1):29-29
The digitization of images has not only led to increasingly sophisticated methods of quantitating information from those images themselves, but also to the development of new physics-based techniques for extracting information from the original specimen and presenting this as visual data in both two and three-dimensional (3D) forms. This evolution of an image-based discipline has reached maturity in Radiology, but it is only just beginning in Pathology. An historical perspective is provided both on the current state of computational imaging in pathology and of the factors that are impeding further progress in the development and application of these approaches. Emphasis is placed on barriers to the dissemination of information in this area. The value of computational imaging in basic and translational research is clear. However, while there are many examples of "virtual diagnostics" in Radiology, there are only relatively few in Pathology. Nevertheless, we can do cellular level analysis of lesions accessible by endoscopic or catheterization procedures, and a number of steps have been taken toward real-time imaging as adjuncts to traditional biopsies. Progress in computational imaging will greatly expand the role of pathologists in clinical medicine as well as research.
Citation: Journal of Pathology Informatics 2015 6(1):29-29
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- The use of virtual microscopy and a wiki in pathology education: Tracking
student use, involvement, and response
Authors: Zev Leifer
Pages: 30 - 30
Abstract: Zev Leifer
Journal of Pathology Informatics 2015 6(1):30-30
Background: The pathology laboratory course at the New York College of Podiatric Medicine involves the use of Virtual Microscopy. The students can scan the whole slide, section by section, and zoom in or out. Methods: Using the advantages of digital pathology, the students can, in addition, access the slide collections from other medical schools and put up normal histology (control) slides side-by-side with the pathology. They can cut and paste and preserve the region of interest that they find. They can edit and annotate their slides. A wiki was created (http://pathlab2014.wikifoundry.com) for the Class of 2014. The students saved, edited and uploaded their slides. In the wiki format, other students could comment, further edit, and even delete the slides. Results: The students studied Basic Mechanisms and System Pathology. During this time, they saved, edited, shared, and uploaded their slides to the wiki. These were available in one full presentation and were also grouped into 16 albums. They were available to all. Student access was followed by Google analytics. At the end of the course, a questionnaire was distributed, assessing their impression of the wiki format and soliciting strengths and weaknesses. Conclusions: The use of a wiki has a number of important advantages in pathology education. It trains the students in the more sophisticated skills that they will use as professional pathologists or as clinicians: (1) Telepathology-it enables them to share slides and discuss observations. (2) Archiving and retrieval - It models the challenge faced by hospitals, diagnostic labs and physicians in maintaining a collection of slides in a form that is easily accessible. (3) Image analysis-familiarity with the wiki format allows them to jump easily to capturing and storing images found in the literature or in a pathologist's report. Experience with the use of a wiki in pathology education has been quite satisfactory from both the faculty and the student's point of view.
Citation: Journal of Pathology Informatics 2015 6(1):30-30
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Comparative study between quantitative digital image analysis and
fluorescence in situ hybridization of breast cancer equivocal human
epidermal growth factor receptors 2 score 2 + cases
Authors: Essam Ayad, Mina Mansy, Dalal Elwi, Mostafa Salem, Mohamed Salama, Klaus Kayser
Pages: 31 - 31
Abstract: Essam Ayad, Mina Mansy, Dalal Elwi, Mostafa Salem, Mohamed Salama, Klaus Kayser
Journal of Pathology Informatics 2015 6(1):31-31
Background: Optimization of workflow for breast cancer samples with equivocal human epidermal growth factor receptors 2 (HER2)/neu score 2 + results in routine practice, remains to be a central focus of the on-going efforts to assess HER2 status. According to the College of American Pathologists/American Society of Clinical Oncology guidelines equivocal HER2/neu score 2 + cases are subject for further testing, usually by fluorescence in situ hybridization (FISH) investigations. It still remains on open question, whether quantitative digital image analysis of HER2 immunohistochemistry (IHC) stained slides can assist in further refining the HER2 score 2 + . Aim of this Work: To assess utility of quantitative digital analysis of IHC stained slides and compare its performance to FISH in cases of breast cancer with equivocal HER2 score 2 + . Materials and Methods: Fifteen specimens (previously diagnosed as breast cancer and was evaluated as HER 2– score 2 +) represented the study population. Contemporary new cuts were prepared for re-evaluation of HER2 immunohistochemical studies and FISH examination. All the cases were digitally scanned by iScan (Produced by BioImagene [Now Roche-Ventana]). The IHC signals of HER2 were measured using an automated image analyzing system (MECES, www.Diagnomx.eu/meces). Finally, a comparative study was done between the results of the FISH and the quantitative analysis of the virtual slides. Results: Three out of the 15 cases with equivocal HER2 score 2 + , turned out to be positive (3 +) by quantitative digital analysis, and 12 were found to be negative in FISH too. Two of these three positive cases proved to be positive with FISH, and only one was negative. Conclusions: Quantitative digital analysis is highly sensitive and relatively specific when compared to FISH in detecting HER2/neu overexpression. Therefore, it represents a potential reliable substitute for FISH in breast cancer cases, which desire further refinement of equivocal IHC results.
Citation: Journal of Pathology Informatics 2015 6(1):31-31
PubDate: Wed,3 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- The need for informatics to support forensic pathology and death
Authors: Bruce Levy
Pages: 32 - 32
Abstract: Bruce Levy
Journal of Pathology Informatics 2015 6(1):32-32
As a result of their practice of medicine, forensic pathologists create a wealth of data regarding the causes of and reasons for sudden, unexpected or violent deaths. This data have been effectively used to protect the health and safety of the general public in a variety of ways despite current and historical limitations. These limitations include the lack of data standards between the thousands of death investigation (DI) systems in the United States, rudimentary electronic information systems for DI, and the lack of effective communications and interfaces between these systems. Collaboration between forensic pathology and clinical informatics is required to address these shortcomings and a path forward has been proposed that will enable forensic pathology to maximize its effectiveness by providing timely and actionable information to public health and public safety agencies.
Citation: Journal of Pathology Informatics 2015 6(1):32-32
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- An optimized color transformation for the analysis of digital images of
hematoxylin & eosin stained slides
Authors: Mark D Zarella, David E Breen, Andrei Plagov, Fernando U Garcia
Pages: 33 - 33
Abstract: Mark D Zarella, David E Breen, Andrei Plagov, Fernando U Garcia
Journal of Pathology Informatics 2015 6(1):33-33
Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.
Citation: Journal of Pathology Informatics 2015 6(1):33-33
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Support system for pathologists and researchers
Authors: Takumi Ishikawa, Junko Takahashi, Mai Kasai, Takayuki Shiina, Yuka Iijima, Hiroshi Takemura, Hiroshi Mizoguchi, Takeshi Kuwata
Pages: 34 - 34
Abstract: Takumi Ishikawa, Junko Takahashi, Mai Kasai, Takayuki Shiina, Yuka Iijima, Hiroshi Takemura, Hiroshi Mizoguchi, Takeshi Kuwata
Journal of Pathology Informatics 2015 6(1):34-34
Aims: In Japan, cancer is the most prevalent cause of death; the number of patients suffering from cancer is increasing. Hence, there is an increased burden on pathologists to make diagnoses. To reduce pathologists' burden, researchers have developed methods of auto-pathological diagnosis. However, virtual slides, which are created when glass slides are digitally scanned, saved in a unique format, and it is difficult for researchers to work on the virtual slides for developing their own image processing method. This paper presents the support system for pathologists and researchers who use auto-pathological diagnosis (P-SSD). Main purpose of P-SSD was to support both of pathologists and researchers. P-SSD consists of several sub-functions that make it easy not only for pathologists to screen pathological images, double-check their diagnoses, and reduce unimportant image data but also for researchers to develop and apply their original image-processing techniques to pathological images. Methods: We originally developed P-SSD to support both pathologists and researchers developing auto-pathological diagnoses systems. Current version of P-SSD consists of five main functions as follows: (i) Loading virtual slides, (ii) making a supervised database, (iii) learning image features, (iv) detecting cancerous areas, (v) displaying results of detection. Results: P-SSD reduces computer memory size random access memory utilization and the processing time required to divide the virtual slides into the smaller-size images compared with other similar software. The maximum observed reduction in computer memory size and reduction in processing time is 97% and 99.94%, respectively. Conclusions: Unlike other vendor-developed software, P-SSD has interoperability and is capable of handling virtual slides in several formats. Therefore, P-SSD can support both of pathologists and researchers, and has many potential applications in both pathological diagnosis and research area.
Citation: Journal of Pathology Informatics 2015 6(1):34-34
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Evaluation of a smartphone for telepathology: Lessons learned
Authors: Paul Fontelo, Fang Liu, Yukako Yagi
Pages: 35 - 35
Abstract: Paul Fontelo, Fang Liu, Yukako Yagi
Journal of Pathology Informatics 2015 6(1):35-35
Background: Mobile networks and smartphones are growing in developing countries. Expert telemedicine consultation will become more convenient and feasible. We wanted to report on our experience in using a smartphone and a 3-D printed adapter for capturing microscopic images. Methods: Images and videos from a gastrointestinal biopsy teaching set of referred cases from the AFIP were captured with an iPhone 5 smartphone fitted with a 3-D printed adapter. Nine pathologists worldwide evaluated the images for quality, adequacy for telepathology consultation, and confidence rendering a diagnosis based on the images viewed on the web. Results: Average Likert scales (ordinal data) for image quality (1=poor, 5=diagnostic) and adequacy for diagnosis (1=No, 5=Yes) had modes of 3 and 4, respectively. Adding a video overview of the specimen improved diagnostic confidence. The mode of confidence in diagnosis based on the images reviewed was four. In 31 instances, reviewers' diagnoses completely agreed with AFIP diagnosis, with partial agreement in 9 and major disagreement in 5. There was strong correlation between image quality and confidence (r = 0.78), image quality and adequacy of image (r = 0.73) and whether images were found adequate when reviewers were confident (r = 0.72). Intraclass Correlation for measuring reliability among the four reviewers who finished a majority of cases was high (quality=0.83, adequacy= 0.76 and confidence=0.92). Conclusions: Smartphones allow pathologists and other image dependent disciplines in low resource areas to transmit consultations to experts anywhere in the world. Improvements in camera resolution and training may mitigate some limitations found in this study.
Citation: Journal of Pathology Informatics 2015 6(1):35-35
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- HPASubC: A suite of tools for user subclassification of human protein
atlas tissue images
Authors: Toby C Cornish, Aravinda Chakravarti, Ashish Kapoor, Marc K Halushka
Pages: 36 - 36
Abstract: Toby C Cornish, Aravinda Chakravarti, Ashish Kapoor, Marc K Halushka
Journal of Pathology Informatics 2015 6(1):36-36
Background: The human protein atlas (HPA) is a powerful proteomic tool for visualizing the distribution of protein expression across most human tissues and many common malignancies. The HPA includes immunohistochemically-stained images from tissue microarrays (TMAs) that cover 48 tissue types and 20 common malignancies. The TMA data are used to provide expression information at the tissue, cellular, and occasionally, subcellular level. The HPA also provides subcellular data from confocal immunofluorescence data on three cell lines. Despite the availability of localization data, many unique patterns of cellular and subcellular expression are not documented. Materials and Methods: To get at this more granular data, we have developed a suite of Python scripts, HPASubC, to aid in subcellular, and cell-type specific classification of HPA images. This method allows the user to download and optimize specific HPA TMA images for review. Then, using a playstation-style video game controller, a trained observer can rapidly step through 10's of 1000's of images to identify patterns of interest. Results: We have successfully used this method to identify 703 endothelial cell (EC) and/or smooth muscle cell (SMCs) specific proteins discovered within 49,200 heart TMA images. This list will assist us in subdividing cardiac gene or protein array data into expression by one of the predominant cell types of the myocardium: Myocytes, SMCs or ECs. Conclusions: The opportunity to further characterize unique staining patterns across a range of human tissues and malignancies will accelerate our understanding of disease processes and point to novel markers for tissue evaluation in surgical pathology.
Citation: Journal of Pathology Informatics 2015 6(1):36-36
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Biomedical imaging ontologies: A survey and proposal for future work
Authors: Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E Kahn, James Overton, John Tomaszewski, Metin Gurcan
Pages: 37 - 37
Abstract: Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E Kahn, James Overton, John Tomaszewski, Metin Gurcan
Journal of Pathology Informatics 2015 6(1):37-37
Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as "cell" or "image" or "tissue" or "microscope") that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.
Citation: Journal of Pathology Informatics 2015 6(1):37-37
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Validation of natural language processing to extract breast cancer
pathology procedures and results
Authors: Arika E Wieneke, Erin J. A. Bowles, David Cronkite, Karen J Wernli, Hongyuan Gao, David Carrell, Diana S. M. Buist
Pages: 38 - 38
Abstract: Arika E Wieneke, Erin J. A. Bowles, David Cronkite, Karen J Wernli, Hongyuan Gao, David Carrell, Diana S. M. Buist
Journal of Pathology Informatics 2015 6(1):38-38
Background: Pathology reports typically require manual review to abstract research data. We developed a natural language processing (NLP) system to automatically interpret free-text breast pathology reports with limited assistance from manual abstraction. Methods: We used an iterative approach of machine learning algorithms and constructed groups of related findings to identify breast-related procedures and results from free-text pathology reports. We evaluated the NLP system using an all-or-nothing approach to determine which reports could be processed entirely using NLP and which reports needed manual review beyond NLP. We divided 3234 reports for development (2910, 90%), and evaluation (324, 10%) purposes using manually reviewed pathology data as our gold standard. Results: NLP correctly coded 12.7% of the evaluation set, flagged 49.1% of reports for manual review, incorrectly coded 30.8%, and correctly omitted 7.4% from the evaluation set due to irrelevancy (i.e. not breast-related). Common procedures and results were identified correctly (e.g. invasive ductal with 95.5% precision and 94.0% sensitivity), but entire reports were flagged for manual review because of rare findings and substantial variation in pathology report text. Conclusions: The NLP system we developed did not perform sufficiently for abstracting entire breast pathology reports. The all-or-nothing approach resulted in too broad of a scope of work and limited our flexibility to identify breast pathology procedures and results. Our NLP system was also limited by the lack of the gold standard data on rare findings and wide variation in pathology text. Focusing on individual, common elements and improving pathology text report standardization may improve performance.
Citation: Journal of Pathology Informatics 2015 6(1):38-38
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Automated image based prominent nucleoli detection
Authors: Choon K Yap, Emarene M Kalaw, Malay Singh, Kian T Chong, Danilo M Giron, Chao-Hui Huang, Li Cheng, Yan N Law, Hwee Kuan Lee
Pages: 39 - 39
Abstract: Choon K Yap, Emarene M Kalaw, Malay Singh, Kian T Chong, Danilo M Giron, Chao-Hui Huang, Li Cheng, Yan N Law, Hwee Kuan Lee
Journal of Pathology Informatics 2015 6(1):39-39
Introduction: Nucleolar changes in cancer cells are one of the cytologic features important to the tumor pathologist in cancer assessments of tissue biopsies. However, inter-observer variability and the manual approach to this work hamper the accuracy of the assessment by pathologists. In this paper, we propose a computational method for prominent nucleoli pattern detection. Materials and Methods: Thirty-five hematoxylin and eosin stained images were acquired from prostate cancer, breast cancer, renal clear cell cancer and renal papillary cell cancer tissues. Prostate cancer images were used for the development of a computer-based automated prominent nucleoli pattern detector built on a cascade farm. An ensemble of approximately 1000 cascades was constructed by permuting different combinations of classifiers such as support vector machines, eXclusive component analysis, boosting, and logistic regression. The output of cascades was then combined using the RankBoost algorithm. The output of our prominent nucleoli pattern detector is a ranked set of detected image patches of patterns of prominent nucleoli. Results: The mean number of detected prominent nucleoli patterns in the top 100 ranked detected objects was 58 in the prostate cancer dataset, 68 in the breast cancer dataset, 86 in the renal clear cell cancer dataset, and 76 in the renal papillary cell cancer dataset. The proposed cascade farm performs twice as good as the use of a single cascade proposed in the seminal paper by Viola and Jones. For comparison, a naive algorithm that randomly chooses a pixel as a nucleoli pattern would detect five correct patterns in the first 100 ranked objects. Conclusions: Detection of sparse nucleoli patterns in a large background of highly variable tissue patterns is a difficult challenge our method has overcome. This study developed an accurate prominent nucleoli pattern detector with the potential to be used in the clinical settings.
Citation: Journal of Pathology Informatics 2015 6(1):39-39
PubDate: Tue,23 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Development of a semi-automated method for subspecialty case distribution
and prediction of intraoperative consultations in surgical pathology
Authors: Raul S Gonzalez, Daniel Long, Omar Hameed
Pages: 40 - 40
Abstract: Raul S Gonzalez, Daniel Long, Omar Hameed
Journal of Pathology Informatics 2015 6(1):40-40
Background: In many surgical pathology laboratories, operating room schedules are prospectively reviewed to determine specimen distribution to different subspecialty services and to predict the number and nature of potential intraoperative consultations for which prior medical records and slides require review. At our institution, such schedules were manually converted into easily interpretable, surgical pathology-friendly reports to facilitate these activities. This conversion, however, was time-consuming and arguably a non-value-added activity. Objective: Our goal was to develop a semi-automated method of generating these reports that improved their readability while taking less time to perform than the manual method. Materials and Methods: A dynamic Microsoft Excel workbook was developed to automatically convert published operating room schedules into different tabular formats. Based on the surgical procedure descriptions in the schedule, a list of linked keywords and phrases was utilized to sort cases by subspecialty and to predict potential intraoperative consultations. After two trial-and-optimization cycles, the method was incorporated into standard practice. Results: The workbook distributed cases to appropriate subspecialties and accurately predicted intraoperative requests. Users indicated that they spent 1-2 h fewer per day on this activity than before, and team members preferred the formatting of the newer reports. Comparison of the manual and semi-automatic predictions showed that the mean daily difference in predicted versus actual intraoperative consultations underwent no statistically significant changes before and after implementation for most subspecialties. Conclusions: A well-designed, lean, and simple information technology solution to determine subspecialty case distribution and prediction of intraoperative consultations in surgical pathology is approximately as accurate as the gold standard manual method and requires less time and effort to generate.
Citation: Journal of Pathology Informatics 2015 6(1):40-40
PubDate: Mon,29 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Content-based image retrieval of digitized histopathology in boosted
spectrally embedded spaces
Authors: Akshay Sridhar, Scott Doyle, Anant Madabhushi
Pages: 41 - 41
Abstract: Akshay Sridhar, Scott Doyle, Anant Madabhushi
Journal of Pathology Informatics 2015 6(1):41-41
Context : Content-based image retrieval (CBIR) systems allow for retrieval of images from within a database that are similar in visual content to a query image. This is useful for digital pathology, where text-based descriptors alone might be inadequate to accurately describe image content. By representing images via a set of quantitative image descriptors, the similarity between a query image with respect to archived, annotated images in a database can be computed and the most similar images retrieved. Recently, non-linear dimensionality reduction methods have become popular for embedding high-dimensional data into a reduced-dimensional space while preserving local object adjacencies, thereby allowing for object similarity to be determined more accurately in the reduced-dimensional space. However, most dimensionality reduction methods implicitly assume, in computing the reduced-dimensional representation, that all features are equally important. Aims : In this paper we present boosted spectral embedding (BoSE), which utilizes a boosted distance metric to selectively weight individual features (based on training data) to subsequently map the data into a reduced-dimensional space. Settings and Design : BoSE is evaluated against spectral embedding (SE) (which employs equal feature weighting) in the context of CBIR of digitized prostate and breast cancer histopathology images. Materials and Methods : The following datasets, which were comprised of a total of 154 hematoxylin and eosin stained histopathology images, were used: (1) Prostate cancer histopathology (benign vs. malignant), (2) estrogen receptor (ER) + breast cancer histopathology (low vs. high grade), and (3) HER2+ breast cancer histopathology (low vs. high levels of lymphocytic infiltration). Statistical Analysis Used : We plotted and calculated the area under precision-recall curves (AUPRC) and calculated classification accuracy using the Random Forest classifier. Results : BoSE outperformed SE both in terms of CBIR-based (area under the precision-recall curve) and classifier-based (classification accuracy) on average across all of the dimensions tested for all three datasets: (1) Prostate cancer histopathology (AUPRC: BoSE = 0.79, SE = 0.63; Accuracy: BoSE = 0.93, SE = 0.80), (2) ER + breast cancer histopathology (AUPRC: BoSE = 0.79, SE = 0.68; Accuracy: BoSE = 0.96, SE = 0.96), and (3) HER2+ breast cancer histopathology (AUPRC: BoSE = 0.54, SE = 0.44; Accuracy: BoSE = 0.93, SE = 0.91). Conclusion : Our results suggest that BoSE could serve as an important tool for CBIR and classification of high-dimensional biomedical data.
Citation: Journal of Pathology Informatics 2015 6(1):41-41
PubDate: Mon,29 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Environmental components and methods for engaging pathology residents in
informatics training
Authors: Christopher A Garcia, Jason M Baron, Bruce A Beckwith, Victor Brodsky, Anand S Dighe, Thomas M Gudewicz, Ji Yeon Kim, Veronica E Klepeis, William J Lane, Roy E Lee, Bruce P Levy, Michael A Mahowald, Diana Mandelker, David S McClintock, Andrew M Quinn, Luigi K Rao, Gregory M Riedlinger, Joseph Rudolf, John R Gilbertson
Pages: 42 - 42
Abstract: Christopher A Garcia, Jason M Baron, Bruce A Beckwith, Victor Brodsky, Anand S Dighe, Thomas M Gudewicz, Ji Yeon Kim, Veronica E Klepeis, William J Lane, Roy E Lee, Bruce P Levy, Michael A Mahowald, Diana Mandelker, David S McClintock, Andrew M Quinn, Luigi K Rao, Gregory M Riedlinger, Joseph Rudolf, John R Gilbertson
Journal of Pathology Informatics 2015 6(1):42-42
Citation: Journal of Pathology Informatics 2015 6(1):42-42
PubDate: Mon,29 Jun 2015
Issue No: Vol. 6, No. 1 (2015)
- Investigation of scanning parameters for thyroid fine needle aspiration
cytology specimens: A pilot study
Authors: Maheswari S Mukherjee, Amber D Donnelly, Elizabeth R Lyden, Whitney R Wedel, Mary F McGaughey, John J Baker, Stanley J Radio
Pages: 43 - 43
Abstract: Maheswari S Mukherjee, Amber D Donnelly, Elizabeth R Lyden, Whitney R Wedel, Mary F McGaughey, John J Baker, Stanley J Radio
Journal of Pathology Informatics 2015 6(1):43-43
Background: Interest in developing more feasible and affordable applications of virtual microscopy in the field of cytology continues to grow. Aims: The aim of this study was to investigate the scanning parameters for the thyroid fine needle aspiration (FNA) cytology specimens. Subjects and Methods: A total of twelve glass slides from thyroid FNA cytology specimens were digitized at ×40 with 1 micron (μ) interval using seven focal plane (FP) levels (Group 1), five FP levels (Group 2), and three FP levels (Group 3) using iScan Coreo Au scanner (Ventana, AZ, USA) producing 36 virtual images (VI). With an average wash out period of 2 days, three participants diagnosed the preannotated cells of Groups 1, 2, and 3 using BioImagene's Image Viewer (version 3.1) (Ventana, Inc., Tucson, AZ, USA), and the corresponding 12 glass slides (Group 4) using conventional light microscopy. Results: All three raters correctly identified and showed complete agreement on the glass and VI for: 86% of the cases at FP Level 3, 83% of the cases at both the FP Levels 5 and 7. The intra-observer concordance between the glass slides and VI for all three raters was highest (97%) for Level 3 and glass, same (94%) for Level 5 and glass; and Level 7 and glass. The inter-rater reliability was found to be highest for the glass slides, and three FP levels (77%), followed by five FP levels (69.5%), and seven FP levels (69.1%). Conclusions: This pilot study found that among the three different FP levels, the VI digitized using three FP levels had slightly higher concordance, intra-observer concordance, and inter-rater reliability. Scanning additional levels above three FP levels did not improve concordance. We believe that there is no added benefit of acquiring five FP levels or more especially when considering the file size, and storage costs. Hence, this study reports that FP level three and 1 μ could be the potential scanning parameters for the thyroid FNA cytology specimens.
Citation: Journal of Pathology Informatics 2015 6(1):43-43
PubDate: Tue,28 Jul 2015
Issue No: Vol. 6, No. 1 (2015)
- Smartphone applications: A contemporary resource for dermatopathology
Authors: Matthew G Hanna, Anil V Parwani, Liron Pantanowitz, Vinod Punjabi, Rajendra Singh
Pages: 44 - 44
Abstract: Matthew G Hanna, Anil V Parwani, Liron Pantanowitz, Vinod Punjabi, Rajendra Singh
Journal of Pathology Informatics 2015 6(1):44-44
Introduction: Smartphone applications in medicine are becoming increasingly prevalent. Given that most pathologists and pathology trainees today use smartphones, an obvious modality for pathology education is through smartphone applications. "MyDermPath" is a novel smartphone application that was developed as an interactive reference tool for dermatology and dermatopathology, available for iOS and Android. Materials and Methods: "MyDermPath" was developed using Apple Xcode and Google Android SDK. Dermatology images (static and virtual slides) were annotated and configured into an algorithmic format. Each image comprised educational data (diagnosis, clinical information, histopathology, special stains, differential diagnosis, clinical management, linked PubMed references). Added functionality included personal note taking, pop quiz, and image upload capabilities. A website was created (http://mydermpath.com) to mirror the app. Results: The application was released in August 2011 and updated in November 2013. More than 1,100 reference diagnoses, with over 2,000 images are available via the application and website. The application has been downloaded approximately 14,000 times. The application is available for use on iOS and Android platforms. Conclusions: Smartphone applications have tremendous potential for advancing pathology education. "MyDermPath" represents an interactive reference tool for dermatology and dermatopathologists.
Citation: Journal of Pathology Informatics 2015 6(1):44-44
PubDate: Tue,28 Jul 2015
Issue No: Vol. 6, No. 1 (2015)
- Use of a data warehouse at an academic medical center for clinical
pathology quality improvement, education, and research
Authors: Matthew D Krasowski, Andy Schriever, Gagan Mathur, John L Blau, Stephanie L Stauffer, Bradley A Ford
Pages: 45 - 45
Abstract: Matthew D Krasowski, Andy Schriever, Gagan Mathur, John L Blau, Stephanie L Stauffer, Bradley A Ford
Journal of Pathology Informatics 2015 6(1):45-45
Background: Pathology data contained within the electronic health record (EHR), and laboratory information system (LIS) of hospitals represents a potentially powerful resource to improve clinical care. However, existing reporting tools within commercial EHR and LIS software may not be able to efficiently and rapidly mine data for quality improvement and research applications. Materials and Methods: We present experience using a data warehouse produced collaboratively between an academic medical center and a private company. The data warehouse contains data from the EHR, LIS, admission/discharge/transfer system, and billing records and can be accessed using a self-service data access tool known as Starmaker. The Starmaker software allows users to use complex Boolean logic, include and exclude rules, unit conversion and reference scaling, and value aggregation using a straightforward visual interface. More complex queries can be achieved by users with experience with Structured Query Language. Queries can use biomedical ontologies such as Logical Observation Identifiers Names and Codes and Systematized Nomenclature of Medicine. Result: We present examples of successful searches using Starmaker, falling mostly in the realm of microbiology and clinical chemistry/toxicology. The searches were ones that were either very difficult or basically infeasible using reporting tools within the EHR and LIS used in the medical center. One of the main strengths of Starmaker searches is rapid results, with typical searches covering 5 years taking only 1-2 min. A "Run Count" feature quickly outputs the number of cases meeting criteria, allowing for refinement of searches before downloading patient-identifiable data. The Starmaker tool is available to pathology residents and fellows, with some using this tool for quality improvement and scholarly projects. Conclusion: A data warehouse has significant potential for improving utilization of clinical pathology testing. Software that can access data warehouse using a straightforward visual interface can be incorporated into pathology training programs.
Citation: Journal of Pathology Informatics 2015 6(1):45-45
PubDate: Tue,28 Jul 2015
Issue No: Vol. 6, No. 1 (2015)
- A conceptual model for translating omic data into clinical action
Authors: Timothy M Herr, Suzette J Bielinski, Erwin Bottinger, Ariel Brautbar, Murray Brilliant, Christopher G Chute, Joshua Denny, Robert R Freimuth, Andrea Hartzler, Joseph Kannry, Isaac S Kohane, Iftikhar J Kullo, Simon Lin, Jyotishman Pathak, Peggy Peissig, Jill Pulley, James Ralston, Luke Rasmussen, Dan Roden, Gerard Tromp, Marc S Williams, Justin Starren
Pages: 46 - 46
Abstract: Timothy M Herr, Suzette J Bielinski, Erwin Bottinger, Ariel Brautbar, Murray Brilliant, Christopher G Chute, Joshua Denny, Robert R Freimuth, Andrea Hartzler, Joseph Kannry, Isaac S Kohane, Iftikhar J Kullo, Simon Lin, Jyotishman Pathak, Peggy Peissig, Jill Pulley, James Ralston, Luke Rasmussen, Dan Roden, Gerard Tromp, Marc S Williams, Justin Starren
Journal of Pathology Informatics 2015 6(1):46-46
Genomic, proteomic, epigenomic, and other "omic" data have the potential to enable precision medicine, also commonly referred to as personalized medicine. The volume and complexity of omic data are rapidly overwhelming human cognitive capacity, requiring innovative approaches to translate such data into patient care. Here, we outline a conceptual model for the application of omic data in the clinical context, called "the omic funnel." This model parallels the classic "Data, Information, Knowledge, Wisdom pyramid" and adds context for how to move between each successive layer. Its goal is to allow informaticians, researchers, and clinicians to approach the problem of translating omic data from bench to bedside, by using discrete steps with clearly defined needs. Such an approach can facilitate the development of modular and interoperable software that can bring precision medicine into widespread practice.
Citation: Journal of Pathology Informatics 2015 6(1):46-46
PubDate: Mon,31 Aug 2015
Issue No: Vol. 6, No. 1 (2015)
- Whole slide image with image analysis of atypical bile duct brushing:
Quantitative features predictive of malignancy
Authors: Brian T Collins, Cody R Weimholt
Pages: 47 - 47
Abstract: Brian T Collins, Cody R Weimholt
Journal of Pathology Informatics 2015 6(1):47-47
Background: Whole slide images (WSIs) involve digitally capturing glass slides for microscopic computer-based viewing and these are amenable to quantitative image analysis. Bile duct (BD) brushing can show morphologic features that are categorized as indeterminate for malignancy. The study aims to evaluate quantitative morphologic features of atypical categories of BD brushing by WSI analysis for the identification of criteria predictive of malignancy. Materials and Methods: Over a 3-year period, BD brush specimens with indeterminate diagnostic categorization (atypical to suspicious) were subjected to WSI analysis. Ten well-visualized groups with morphologic atypical features were selected per case and had the quantitative analysis performed for group area, individual nuclear area, the number of nuclei per group, N: C ratio and nuclear size differential. Results: There were 28 cases identified with 17 atypical and 11 suspicious. The average nuclear area was 63.7 µm2 for atypical and 80.1 µm2 for suspicious (+difference 16.4 µm2; P = 0.002). The nuclear size differential was 69.7 µm2 for atypical and 88.4 µm2 for suspicious (+difference 18.8 µm2; P = 0.009). An average nuclear area >70 µm2 had a 3.2 risk ratio for suspicious categorization. Conclusion: The quantitative criteria findings as measured by image analysis on WSI showed that cases categorized as suspicious had more nuclear size pleomorphism (+18.8 µm2) and larger nuclei (+16.4 µm2) than those categorized as atypical. WSI with morphologic image analysis can demonstrate quantitative statistically significant differences between atypical and suspicious BD brushings and provide objective criteria that support the diagnosis of carcinoma.
Citation: Journal of Pathology Informatics 2015 6(1):47-47
PubDate: Mon,31 Aug 2015
Issue No: Vol. 6, No. 1 (2015)
- TissueCypher™: A systems biology approach to anatomic
Authors: Jeffrey W Prichard, Jon M Davison, Bruce B Campbell, Kathleen A Repa, Lia M Reese, Xuan M Nguyen, Jinhong Li, Tyler Foxwell, Lansing D Taylor, Rebecca J Critchley-Thorne
Pages: 48 - 48
Abstract: Jeffrey W Prichard, Jon M Davison, Bruce B Campbell, Kathleen A Repa, Lia M Reese, Xuan M Nguyen, Jinhong Li, Tyler Foxwell, Lansing D Taylor, Rebecca J Critchley-Thorne
Journal of Pathology Informatics 2015 6(1):48-48
Background: Current histologic methods for diagnosis are limited by intra- and inter-observer variability. Immunohistochemistry (IHC) methods are frequently used to assess biomarkers to aid diagnoses, however, IHC staining is variable and nonlinear and the manual interpretation is subjective. Furthermore, the biomarkers assessed clinically are typically biomarkers of epithelial cell processes. Tumors and premalignant tissues are not composed only of epithelial cells but are interacting systems of multiple cell types, including various stromal cell types that are involved in cancer development. The complex network of the tissue system highlights the need for a systems biology approach to anatomic pathology, in which quantification of system processes is combined with informatics tools to produce actionable scores to aid clinical decision-making. Aims: Here, we describe a quantitative, multiplexed biomarker imaging approach termed TissueCypher™ that applies systems biology to anatomic pathology. Applications of TissueCypher™ in understanding the tissue system of Barrett's esophagus (BE) and the potential use as an adjunctive tool in the diagnosis of BE are described. Patients and Methods: The TissueCypher™ Image Analysis Platform was used to assess 14 epithelial and stromal biomarkers with known diagnostic significance in BE in a set of BE biopsies with nondysplastic BE with reactive atypia (RA, n = 22) and Barrett's with high-grade dysplasia (HGD, n = 17). Biomarker and morphology features were extracted and evaluated in the confirmed BE HGD cases versus the nondysplastic BE cases with RA. Results: Multiple image analysis features derived from epithelial and stromal biomarkers, including immune biomarkers and morphology, showed significant differences between HGD and RA. Conclusions: The assessment of epithelial cell abnormalities combined with an assessment of cellular changes in the lamina propria may serve as an adjunct to conventional pathology in the assessment of BE.
Citation: Journal of Pathology Informatics 2015 6(1):48-48
PubDate: Mon,31 Aug 2015
Issue No: Vol. 6, No. 1 (2015)
- Validation of whole slide imaging for frozen section diagnosis in surgical
Authors: Thomas W Bauer, Renee J Slaw, Jesse K McKenney, Deepa T Patil
Pages: 49 - 49
Abstract: Thomas W Bauer, Renee J Slaw, Jesse K McKenney, Deepa T Patil
Journal of Pathology Informatics 2015 6(1):49-49
Background: Whole slide imaging (WSI) using high-resolution scanners is gaining acceptance as a platform for consultation as well as for frozen section (FS) evaluation in surgical pathology. We report results of an intra-observer concordance study comparing evaluation of WSI of scanned FS microscope slides with the original interpretation of the same microscope slides after an average lag time of approximately 1-year. Methods: A total of 70 FS cases (148 microscope slides) originally interpreted by 2 pathologists were scanned at ×20 using Aperio CS2 scanner (Leica Biosystems, San Diego, CA, USA). Reports were redacted such that the study pathologists reviewed images using eSlide Manager Healthcare Network application (Leica Biosystems) accompanied by the same clinical information available at the time of original FS evaluation. Discrepancies between the original FS diagnosis and WSI diagnosis were categorized as major (impacted patient care) or minor (no impact on patient care). Results: Lymph nodes, margins for head and neck cancer resections, and arthroplasty specimens to exclude infection, were the most common FS specimens. The average wash-out interval was 380 days (range: 303–466 days). There was one major discrepancy (1.4% of 70 cases) where the original FS was interpreted as severe squamous dysplasia, and the WSI FS diagnosis was mild dysplasia. There were two minor discrepancies; one where the original FS was called focal moderate squamous dysplasia and WSI FS diagnosis was negative for dysplasia. The second case was an endometrial adenocarcinoma that was originally interpreted as Federation of Gynecology and Obstetrics (FIGO) Grade I, while the WSI FS diagnosis was FIGO Grade II. Conclusions: These findings validate and support the use of WSI to provide interpretation of FS in our network of affiliated hospitals and ambulatory surgery centers.
Citation: Journal of Pathology Informatics 2015 6(1):49-49
PubDate: Mon,31 Aug 2015
Issue No: Vol. 6, No. 1 (2015)
- Practical considerations in genomic decision support: The eMERGE
Authors: Timothy M Herr, Suzette J Bielinski, Erwin Bottinger, Ariel Brautbar, Murray Brilliant, Christopher G Chute, Beth L Cobb, Joshua C Denny, Hakon Hakonarson, Andrea L Hartzler, George Hripcsak, Joseph Kannry, Isaac S Kohane, Iftikhar J Kullo, Simon Lin, Shannon Manzi, Keith Marsolo, Casey Lynnette Overby, Jyotishman Pathak, Peggy Peissig, Jill Pulley, James Ralston, Luke Rasmussen, Dan M Roden, Gerard Tromp, Timothy Uphoff, Chunhua Weng, Wendy Wolf, Marc S Williams, Justin Starren
Pages: 50 - 50
Abstract: Timothy M Herr, Suzette J Bielinski, Erwin Bottinger, Ariel Brautbar, Murray Brilliant, Christopher G Chute, Beth L Cobb, Joshua C Denny, Hakon Hakonarson, Andrea L Hartzler, George Hripcsak, Joseph Kannry, Isaac S Kohane, Iftikhar J Kullo, Simon Lin, Shannon Manzi, Keith Marsolo, Casey Lynnette Overby, Jyotishman Pathak, Peggy Peissig, Jill Pulley, James Ralston, Luke Rasmussen, Dan M Roden, Gerard Tromp, Timothy Uphoff, Chunhua Weng, Wendy Wolf, Marc S Williams, Justin Starren
Journal of Pathology Informatics 2015 6(1):50-50
Background: Genomic medicine has the potential to improve care by tailoring treatments to the individual. There is consensus in the literature that pharmacogenomics (PGx) may be an ideal starting point for real-world implementation, due to the presence of well-characterized drug-gene interactions. Clinical Decision Support (CDS) is an ideal avenue by which to implement PGx at the bedside. Previous literature has established theoretical models for PGx CDS implementation and discussed a number of anticipated real-world challenges. However, work detailing actual PGx CDS implementation experiences has been limited. Anticipated challenges include data storage and management, system integration, physician acceptance, and more. Methods: In this study, we analyzed the experiences of ten members of the Electronic Medical Records and Genomics (eMERGE) Network, and one affiliate, in their attempts to implement PGx CDS. We examined the resulting PGx CDS system characteristics and conducted a survey to understand the unanticipated implementation challenges sites encountered. Results: Ten sites have successfully implemented at least one PGx CDS rule in the clinical setting. The majority of sites elected to create an Omic Ancillary System (OAS) to manage genetic and genomic data. All sites were able to adapt their existing CDS tools for PGx knowledge. The most common and impactful delays were not PGx-specific issues. Instead, they were general IT implementation problems, with top challenges including team coordination/communication and staffing. The challenges encountered caused a median total delay in system go-live of approximately two months. Conclusions: These results suggest that barriers to PGx CDS implementations are generally surmountable. Moreover, PGx CDS implementation may not be any more difficult than other healthcare IT projects of similar scope, as the most significant delays encountered were not unique to genomic medicine. These are encouraging results for any institution considering implementing a PGx CDS tool, and for the advancement of genomic medicine.
Citation: Journal of Pathology Informatics 2015 6(1):50-50
PubDate: Mon,28 Sep 2015
Issue No: Vol. 6, No. 1 (2015)
- Support patient search on pathology reports with interactive online
learning based data extraction
Authors: Shuai Zheng, James J Lu, Christina Appin, Daniel Brat, Fusheng Wang
Pages: 51 - 51
Abstract: Shuai Zheng, James J Lu, Christina Appin, Daniel Brat, Fusheng Wang
Journal of Pathology Informatics 2015 6(1):51-51
Background: Structural reporting enables semantic understanding and prompt retrieval of clinical findings about patients. While synoptic pathology reporting provides templates for data entries, information in pathology reports remains primarily in narrative free text form. Extracting data of interest from narrative pathology reports could significantly improve the representation of the information and enable complex structured queries. However, manual extraction is tedious and error-prone, and automated tools are often constructed with a fixed training dataset and not easily adaptable. Our goal is to extract data from pathology reports to support advanced patient search with a highly adaptable semi-automated data extraction system, which can adjust and self-improve by learning from a user's interaction with minimal human effort. Methods : We have developed an online machine learning based information extraction system called IDEAL-X. With its graphical user interface, the system's data extraction engine automatically annotates values for users to review upon loading each report text. The system analyzes users' corrections regarding these annotations with online machine learning, and incrementally enhances and refines the learning model as reports are processed. The system also takes advantage of customized controlled vocabularies, which can be adaptively refined during the online learning process to further assist the data extraction. As the accuracy of automatic annotation improves overtime, the effort of human annotation is gradually reduced. After all reports are processed, a built-in query engine can be applied to conveniently define queries based on extracted structured data. Results: We have evaluated the system with a dataset of anatomic pathology reports from 50 patients. Extracted data elements include demographical data, diagnosis, genetic marker, and procedure. The system achieves F-1 scores of around 95% for the majority of tests. Conclusions: Extracting data from pathology reports could enable more accurate knowledge to support biomedical research and clinical diagnosis. IDEAL-X provides a bridge that takes advantage of online machine learning based data extraction and the knowledge from human's feedback. By combining iterative online learning and adaptive controlled vocabularies, IDEAL-X can deliver highly adaptive and accurate data extraction to support patient search.
Citation: Journal of Pathology Informatics 2015 6(1):51-51
PubDate: Mon,28 Sep 2015
Issue No: Vol. 6, No. 1 (2015)
- Working toward consensus among professionals in the identification of
classical cervical cytomorphological characteristics in whole slide images
Authors: Odille Bongaerts, Paul J van Diest, Math Pieters, Marius Nap
Pages: 52 - 52
Abstract: Odille Bongaerts, Paul J van Diest, Math Pieters, Marius Nap
Journal of Pathology Informatics 2015 6(1):52-52
Introduction: Cervical cancer is one of the most common causes of death in women worldwide. [1] The introduction of cervical cytology in screening programs is an effective way for early detection and treatment of cervical precancerous lesions. Conventional screening of cervical cytology slides is still considered the current "gold standard" for the assessment of proficiency in becoming a cytotechnician, but diagnosis using digital whole slide images (WSI) may offer many advantages. Materials and Methods: In this study, we have used a selection of WSI from thin-layer specimens of the most common cervical infections and (pre) neoplastic lesions, and hypothesized that weekly WSI based case-meetings would help to obtain optimal acceptance of the new digital workflow in daily pathology practice. A questionnaire, before and after the test period was used to study the effect of our approach. Results: The participants clearly had to go through a learning curve to get accustomed to viewing WSI. In the beginning, there was a little self-confidence in recognizing classical cervical cytomorphological features in the WSI, and there were complaints about the speed of viewing and insufficient Z-resolution for cell groups. Adjusting the Z-stack settings resulted in better three-dimensional information due to better focusing options. Weekly meetings appeared to be instrumental in the implementation process, as participants had to select and present WSI from thematic cases themselves, and thereby, got used to viewing WSI. Some WSI were replaced by better ones until a final set of 45 representatives WSI remained. Eventually, the consensus was reached among all participants that cytomorphological features in WSI from thin-layers cervical specimens could comparably be appreciated in WSI as by conventional microscopy. The selection of 45 WSI was now used to create a digital WSI based reference atlas to support further studies. Conclusion: We have obtained consensus between professionals that WSI from cervical cytology can be used to identify cytomorphological features, necessary for diagnosis. In addition, we observed that active participation of professionals had a positive effect on the overall acceptance of WSI and was important in the change management.
Citation: Journal of Pathology Informatics 2015 6(1):52-52
PubDate: Mon,28 Sep 2015
Issue No: Vol. 6, No. 1 (2015)
- Rapid evaluation of fresh ex vivo kidney tissue with full-field optical
coherence tomography
Authors: Manu Jain, Brian D Robinson, Bekheit Salamoon, Olivier Thouvenin, Claude Boccara, Sushmita Mukherjee
Pages: 53 - 53
Abstract: Manu Jain, Brian D Robinson, Bekheit Salamoon, Olivier Thouvenin, Claude Boccara, Sushmita Mukherjee
Journal of Pathology Informatics 2015 6(1):53-53
Background: Full-field optical coherence tomography (FFOCT) is a real-time imaging technique that rapidly generates images reminiscent of histology without any tissue processing, warranting its exploration for evaluation of ex vivo kidney tissue. Methods: Fresh tissue sections from tumor and adjacent nonneoplastic kidney (n = 25 nephrectomy specimens; clear cell renal cell carcinoma (CCRCC) = 12, papillary RCC (PRCC) = 4, chromophobe RCC (ChRCC) = 4, papillary urothelial carcinoma (PUC) = 1, angiomyolipoma (AML) = 2 and cystic nephroma = 2) were imaged with a commercial FFOCT device. Sections were submitted for routine histopathological diagnosis. Results: Glomeruli, tubules, interstitium, and blood vessels were identified in nonneoplastic tissue. In tumor sections, the normal architecture was completely replaced by either sheets of cells/trabeculae or papillary structures. The former pattern was seen predominantly in CCRCC/ChRCC and the latter in PRCC/PUC (as confirmed on H&E). Although the cellular details were not very prominent at this resolution, we could identify unique cytoplasmic signatures in some kidney tumors. For example, the hyper-intense punctate signal in the cytoplasm of CRCC represents glycogen/lipid, large cells with abundant hyper-intense cytoplasm representing histiocytes in PRCC, and signal-void large polygonal cell representing adipocytes in AML. According to a blinded analysis was performed by an uropathologist, all nonneoplastic tissues were differentiated from neoplastic tissues. Further, all benign tumors were called benign and malignant were called malignant. A diagnostic accuracy of 80% was obtained in subtyping the tumors. Conclusion: The ability of FFOCT to reliably differentiate nonneoplastic from neoplastic tissue and identify some tumor types makes it a valuable tool for rapid evaluation of ex vivo kidney tissue e.g. for intraoperative margin assessment and kidney biopsy adequacy. Recently, higher resolution images were achieved using an experimental FFOCT setup. This setup has the potential to further increase the diagnostic accuracy of FFOCT.
Citation: Journal of Pathology Informatics 2015 6(1):53-53
PubDate: Mon,28 Sep 2015
Issue No: Vol. 6, No. 1 (2015)
- Cytopathology whole slide images and virtual microscopy adaptive
tutorials: A software pilot
Authors: Simone L Van Es, Wendy M Pryor, Zack Belinson, Elizabeth L Salisbury, Gary M Velan
Pages: 54 - 54
Abstract: Simone L Van Es, Wendy M Pryor, Zack Belinson, Elizabeth L Salisbury, Gary M Velan
Journal of Pathology Informatics 2015 6(1):54-54
Background: The constant growth in the body of knowledge in medicine requires pathologists and pathology trainees to engage in continuing education. Providing them with equitable access to efficient and effective forms of education in pathology (especially in remote and rural settings) is important, but challenging. Methods: We developed three pilot cytopathology virtual microscopy adaptive tutorials (VMATs) to explore a novel adaptive E-learning platform (AeLP) which can incorporate whole slide images for pathology education. We collected user feedback to further develop this educational material and to subsequently deploy randomized trials in both pathology specialist trainee and also medical student cohorts. Cytopathology whole slide images were first acquired then novel VMATs teaching cytopathology were created using the AeLP, an intelligent tutoring system developed by Smart Sparrow. The pilot was run for Australian pathologists and trainees through the education section of Royal College of Pathologists of Australasia website over a period of 9 months. Feedback on the usability, impact on learning and any technical issues was obtained using 5-point Likert scale items and open-ended feedback in online questionnaires. Results: A total of 181 pathologists and pathology trainees anonymously attempted the three adaptive tutorials, a smaller proportion of whom went on to provide feedback at the end of each tutorial. VMATs were perceived as effective and efficient E-learning tools for pathology education. User feedback was positive. There were no significant technical issues. Conclusion: During this pilot, the user feedback on the educational content and interface and the lack of technical issues were helpful. Large scale trials of similar online cytopathology adaptive tutorials were planned for the future.
Citation: Journal of Pathology Informatics 2015 6(1):54-54
PubDate: Mon,28 Sep 2015
Issue No: Vol. 6, No. 1 (2015)
- Utility of telepathology as a consultation tool between an off-site
surgical pathology suite and affiliated hospitals in the frozen section
diagnosis of lung neoplasms
Authors: Taisia Vitkovski, Tawfiqul Bhuiya, Michael Esposito
Pages: 55 - 55
Abstract: Taisia Vitkovski, Tawfiqul Bhuiya, Michael Esposito
Journal of Pathology Informatics 2015 6(1):55-55
Background: Increasingly, as in our institution, operating rooms are located in hospitals and the pathology suite is located at a distant location because of off-site consolidation of pathology services. Telepathology is a technology which bridges the gap between pathologists and offers a means to obtain a consultation remotely. We aimed to evaluate the utility of telepathology as a means to assist the pathologist at the time of intraoperative consultation of lung nodules when a subspecialty pathologist is not available to directly review the slide. Methods: Cases of lung nodules suspicious for a neoplasm were included. Frozen sections were prepared in the usual manner. The pathologists on the intraoperative consultation service at two of our system hospitals notified the thoracic pathologist of each case after rendering a preliminary diagnosis. The consultation was performed utilizing a Nikon™ Digital Sight camera and web-based Remote Medical Technologies™ software with live video streaming directed by the host pathologist. The thoracic pathologist rendered a diagnosis without knowledge of the preliminary interpretation then discussed the interpretation with the frozen section pathologist. The interpretations were compared with the final diagnosis rendered after sign-out. Results: One hundred and three consecutive cases were included. The frozen section pathologist and a thoracic pathologist had concordant diagnoses in 93 cases (90.2%), discordant diagnoses in nine cases (8.7%), and one case in which both deferred. There was an agreement between the thoracic pathologist's diagnosis and the final diagnosis in 98% of total cases including 8/9 (88.9%) of the total discordant cases. In two cases, if the thoracic pathologist had not been consulted, the patient would have been undertreated. Conclusions: We have shown that telepathology is an excellent consultation tool in the frozen section diagnosis of lung nodules.
Citation: Journal of Pathology Informatics 2015 6(1):55-55
PubDate: Wed,28 Oct 2015
Issue No: Vol. 6, No. 1 (2015)
- Diagnostic performance on briefly presented digital pathology images
Authors: Joseph P Houghton, Bruce R Smoller, Niamh Leonard, Michael R Stevenson, Tim Dornan
Pages: 56 - 56
Abstract: Joseph P Houghton, Bruce R Smoller, Niamh Leonard, Michael R Stevenson, Tim Dornan
Journal of Pathology Informatics 2015 6(1):56-56
Background: Identifying new and more robust assessments of proficiency/expertise (finding new "biomarkers of expertise") in histopathology is desirable for many reasons. Advances in digital pathology permit new and innovative tests such as flash viewing tests and eye tracking and slide navigation analyses that would not be possible with a traditional microscope. The main purpose of this study was to examine the usefulness of time-restricted testing of expertise in histopathology using digital images. Methods: 19 novices (undergraduate medical students), 18 intermediates (trainees), and 19 experts (consultants) were invited to give their opinion on 20 general histopathology cases after 1 s and 10 s viewing times. Differences in performance between groups were measured and the internal reliability of the test was calculated. Results: There were highly significant differences in performance between the groups using the Fisher's least significant difference method for multiple comparisons. Differences between groups were consistently greater in the 10-s than the 1-s test. The Kuder-Richardson 20 internal reliability coefficients were very high for both tests: 0.905 for the 1-s test and 0.926 for the 10-s test. Consultants had levels of diagnostic accuracy of 72% at 1 s and 83% at 10 s. Conclusions: Time-restricted tests using digital images have the potential to be extremely reliable tests of diagnostic proficiency in histopathology. A 10-s viewing test may be more reliable than a 1-s test. Over-reliance on "at a glance" diagnoses in histopathology is a potential source of medical error due to over-confidence bias and premature closure.
Citation: Journal of Pathology Informatics 2015 6(1):56-56
PubDate: Wed,28 Oct 2015
Issue No: Vol. 6, No. 1 (2015)
- Analysis of the impact of high-resolution monitors in digital pathology
Pages: 57 - 57
Abstract: Marcial García Rojo, Gloria Bueno
Journal of Pathology Informatics 2015 6(1):57-57
Citation: Journal of Pathology Informatics 2015 6(1):57-57
PubDate: Wed,28 Oct 2015
Issue No: Vol. 6, No. 1 (2015)
- Response to Rojo and Bueno: "Analysis of the impact of high
resolution monitors in digital pathology"
Authors: Rebecca Randell, Roy A Ruddle, Rhys G Thomas, Darren Treanor
Pages: 58 - 58
Abstract: Rebecca Randell, Roy A Ruddle, Rhys G Thomas, Darren Treanor
Journal of Pathology Informatics 2015 6(1):58-58
Citation: Journal of Pathology Informatics 2015 6(1):58-58
PubDate: Wed,28 Oct 2015
Issue No: Vol. 6, No. 1 (2015)
- Inclusion probability for DNA mixtures is a subjective one-sided match
statistic unrelated to identification information
Authors: Mark William Perlin
Pages: 59 - 59
Abstract: Mark William Perlin
Journal of Pathology Informatics 2015 6(1):59-59
Background: DNA mixtures of two or more people are a common type of forensic crime scene evidence. A match statistic that connects the evidence to a criminal defendant is usually needed for court. Jurors rely on this strength of match to help decide guilt or innocence. However, the reliability of unsophisticated match statistics for DNA mixtures has been questioned. Materials and Methods: The most prevalent match statistic for DNA mixtures is the combined probability of inclusion (CPI), used by crime labs for over 15 years. When testing 13 short tandem repeat (STR) genetic loci, the CPI -1 value is typically around a million, regardless of DNA mixture composition. However, actual identification information, as measured by a likelihood ratio (LR), spans a much broader range. This study examined probability of inclusion (PI) mixture statistics for 517 locus experiments drawn from 16 reported cases and compared them with LR locus information calculated independently on the same data. The log(PI -1 ) values were examined and compared with corresponding log(LR) values. Results: The LR and CPI methods were compared in case examples of false inclusion, false exclusion, a homicide, and criminal justice outcomes. Statistical analysis of crime laboratory STR data shows that inclusion match statistics exhibit a truncated normal distribution having zero center, with little correlation to actual identification information. By the law of large numbers (LLN), CPI -1 increases with the number of tested genetic loci, regardless of DNA mixture composition or match information. These statistical findings explain why CPI is relatively constant, with implications for DNA policy, criminal justice, cost of crime, and crime prevention. Conclusions: Forensic crime laboratories have generated CPI statistics on hundreds of thousands of DNA mixture evidence items. However, this commonly used match statistic behaves like a random generator of inclusionary values, following the LLN rather than measuring identification information. A quantitative CPI number adds little meaningful information beyond the analyst's initial qualitative assessment that a person's DNA is included in a mixture. Statistical methods for reporting on DNA mixture evidence should be scientifically validated before they are relied upon by criminal justice.
Citation: Journal of Pathology Informatics 2015 6(1):59-59
PubDate: Wed,28 Oct 2015
Issue No: Vol. 6, No. 1 (2015)
- Prediction of primary breast cancer size and T-stage using micro-computed
tomography in lumpectomy specimens
Authors: Wafa M Sarraj, Rong Tang, Anas L Najjar, Molly Griffin, Anthony H Bui, Alan Zambeli-Ljepovic, Mike Senter-Zapata, Maya Lewin-Berlin, Leopoldo Fernandez, Juliette Buckley, Amy Ly, Elena Brachtel, Owen Aftreth, John Gilbertson, Yukako Yagi, Michele Gadd, Kevin S Hughes, Barbara L Smith, James S Michaelson
Pages: 60 - 60
Abstract: Wafa M Sarraj, Rong Tang, Anas L Najjar, Molly Griffin, Anthony H Bui, Alan Zambeli-Ljepovic, Mike Senter-Zapata, Maya Lewin-Berlin, Leopoldo Fernandez, Juliette Buckley, Amy Ly, Elena Brachtel, Owen Aftreth, John Gilbertson, Yukako Yagi, Michele Gadd, Kevin S Hughes, Barbara L Smith, James S Michaelson
Journal of Pathology Informatics 2015 6(1):60-60
Background: Histopathology is the only accepted method to measure and stage the breast tumor size. However, there is a need to find another method to measure and stage the tumor size when the pathological assessment is not available. Micro-computed tomography. (micro-CT) has the ability to measure tumor in three dimensions in an intact lumpectomy specimen. In this study, we aimed to determine the accuracy of micro-CT to measure and stage the primary tumor size in breast lumpectomy specimens, as compared to the histopathology. Materials and Methods: Seventy-two women who underwent lumpectomy surgery at the Massachusetts General Hospital Department of Surgery from June 2011 to September 2011, and from August 2013 to December 2013 participated in this study. The lumpectomy specimens were scanned using micro-CT followed by routine pathological processing. The maximum dimension of the invasive breast tumor was obtained from the micro-CT image and was compared to the corresponding pathology report for each subject. Results: The invasive tumor size measurement by micro-CT was underestimated in 24. cases. (33%), overestimated in 37. cases. (51%), and matched it exactly in 11. cases. (15%) compared to the histopathology measurement for all the cases. However, micro-CT T.stage classification differed from histopathology in only 11. (15.2%) with 6. cases. (8.3%) classified as a higher stage by micro-CT, and 5. cases. (6.9%) classified as lower compared to histopathology. In addition, micro-CT demonstrated a statically significant strong agreement (κ =0.6, P < 0.05) with pathological tumor size and staging for invasive ductal carcinoma. (IDC) group. In contrast, there was no agreement. (κ = .2, P = 0.67) between micro-CT and pathology in estimating and staging tumor size for invasive lobular carcinoma. (ILC) group. This could be explained by a small sample size. (7) for ILC group. Conclusions: Micro-CT is a promising modality for measuring and staging the IDC.
Citation: Journal of Pathology Informatics 2015 6(1):60-60
PubDate: Fri,27 Nov 2015
Issue No: Vol. 6, No. 1 (2015)
- General pathologist-helper: The new medical app about general pathology
Pages: 61 - 61
Abstract: Iván Fernandez-Vega
Journal of Pathology Informatics 2015 6(1):61-61
Introduction: Smartphone applications (apps) have become increasingly prevalent in medicine. Due to most pathologists, pathology trainees, technicians, and medical students use smartphones; apps can be a different way for general pathology education. "General pathologist-helper (GP-HELPER)" is a novel app developed as a reference tool in general pathology and especially for general pathologists, developed for Android and iOS platforms. Materials and Methods: "GP-HELPER," was created using Mobincube website platform. This tool also integrates "FORUM GP-HELPER," an external website created using Miarroba website (http://forum-gp-helper.mboards.com) and "COMMUNITY GP-HELPER" a multichannel chat created using Chatango website platform. Results: The application was released in July 2015, and it is been periodically updated since then. The app has permanent information (offline data) about different pathology protocols (TNM latest edition, protocols regarding management of tumors of unknown primary origin, and flowcharts for some of the most difficult tumors to diagnose) and a database with more than 5000 immunohistochemistry results from different tumors. Online data have links to more than 1100 reference pathology video lectures, 250 antibodies information, more than 70 pathology association websites, 46 pathology providers, and 78 outstanding pathology journal websites. Besides this information, the app has two interactive places such as "FORUM GP-HELPER" and "COMMUNITY GP-HELPER" that let users to stay in touch everywhere and every time. Expert consult section is also available. Conclusions: "GP-HELPER" pretends to integrate offline and online data about pathology with two interactive external places in order to represent a reference tool for general pathologists and associate members.
Citation: Journal of Pathology Informatics 2015 6(1):61-61
PubDate: Fri,27 Nov 2015
Issue No: Vol. 6, No. 1 (2015)
- Extraction and analysis of discrete synoptic pathology report data using R
Authors: Alexander Boag
Pages: 62 - 62
Abstract: Alexander Boag
Journal of Pathology Informatics 2015 6(1):62-62
Background: Synoptic pathology reports can serve as a rich source of cancer information, particularly when the content is available as discrete electronic data fields. Our institution generates such reports as part of a province wide program in Ontario but the resulting data is not easily extracted and analyzed at the local level. Methods: A low cost system was developed using the open sourced and freely available R scripting/data analysis environment to parse synoptic report results into a dataframe and perform basic summary statistics. Results: As a pilot project text reports from 427 prostate needle biopsies were successfully read into R and the data elements split out and converted into appropriated data classes for analysis. Conclusion: This approach provides a simple solution at minimal cost that can make discrete synoptic report data readily available for quality assurance and research activities.
Citation: Journal of Pathology Informatics 2015 6(1):62-62
PubDate: Fri,27 Nov 2015
Issue No: Vol. 6, No. 1 (2015)
- International telepathology consultation: Three years of experience
between the University of Pittsburgh Medical Center and KingMed
Diagnostics in China
Authors: Chengquan Zhao, Tao Wu, Xiangdong Ding, Anil V Parwani, Hualin Chen, Jeffrey McHugh, Anthony Piccoli, Qinling Xie, Gonzalo Romero Lauro, Xiaodong Feng, Douglas J Hartman, Raja R Seethala, Shangwei Wu, Samuel Yousem, Yaoming Liang, Liron Pantanowitz
Pages: 63 - 63
Abstract: Chengquan Zhao, Tao Wu, Xiangdong Ding, Anil V Parwani, Hualin Chen, Jeffrey McHugh, Anthony Piccoli, Qinling Xie, Gonzalo Romero Lauro, Xiaodong Feng, Douglas J Hartman, Raja R Seethala, Shangwei Wu, Samuel Yousem, Yaoming Liang, Liron Pantanowitz
Journal of Pathology Informatics 2015 6(1):63-63
Background: Telepathology is increasingly being employed to support diagnostic consultation services. Prior publications have addressed technology aspects for telepathology, whereas this paper will address the clinical telepathology experience of KingMed Diagnostics, the largest independent pathology medical laboratory in China. Beginning in 2012 the University of Pittsburgh Medical Center (UPMC) and KingMed Diagnostics partnered to establish an international telepathology consultation service. Materials and Methods: This is a retrospective study that summarizes the telepathology experience and diagnostic consultation results between UPMC and KingMed over a period of 3 years from January 2012 to December 2014. Results: A total of 1561 cases were submitted for telepathology consultation including 144 cases in 2012, 614 cases in 2013, and 803 in 2014. Most of the cases (61.4%) submitted were referred by pathologists, 36.9% by clinicians, and 1.7% by patients in China. Hematopathology received the most cases (23.7%), followed by bone/soft tissue (21.0%) and gynecologic/breast (20.2%) subspecialties. Average turnaround time (TAT) per case was 5.4 days, which decreased from 6.8 days in 2012 to 5.0 days in 2014. Immunostains were required for most of the cases. For some difficult cases, more than one round of immunostains was needed, which extended the TAT. Among 855 cases (54.7%) where a primary diagnosis or impression was provided by the referring local hospitals in China, the final diagnoses rendered by UPMC pathologists were identical in 25.6% of cases and significantly modified (treatment plan altered) in 50.8% of cases. Conclusion: These results indicate that international telepathology consultation can significantly improve patient care by facilitating access to pathology expertise. The success of this international digital consultation service was dependent on strong commitment and support from leadership, information technology expertise, and dedicated pathologists who understood the language and culture on both sides. Lack of clinical information, missing gross pathology descriptions, and insufficient tissue sections submitted for evaluation were the main reasons for indefinite diagnoses. The overall experience encourages international telepathology practice for second opinions.
Citation: Journal of Pathology Informatics 2015 6(1):63-63
PubDate: Fri,27 Nov 2015
Issue No: Vol. 6, No. 1 (2015)
- Barriers and facilitators to adoption of soft copy interpretation from the
user perspective: Lessons learned from filmless radiology for slideless
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- Global manipulation of digital images can lead to variation in cytological
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
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
Issue No: Vol. 2, No. 1 (2011)
- Reducing patient identification errors related to glucose point-of-care
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
Issue No: Vol. 2, No. 1 (2011)
- Standardization in digital pathology: Supplement 145 of the DICOM
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- Digital slides and ACGME resident competencies in anatomic pathology: An
altered paradigm for acquisition and assessment
Authors: Lewis A Hassell, Kar-Ming Fung, Brad Chaser
Pages: 27 - 27
Abstract: Lewis A Hassell, Kar-Ming Fung, Brad Chaser
Journal of Pathology Informatics 2011 2(1):27-27
Whole slide digital imaging technology has matured considerably over the past decade. Applications in pathology education are widespread and are rapidly transforming the manner in which medical students learn pathology and histology, and they have a novel and significant impact on postgraduate continuing medical education. Whole slide digital images for use in pathology graduate education have been slower in adoption and remain much less widespread. Emphasis on professional competency by the Accreditation Council on Graduate Medical Education (ACGME) and credentialing organizations, however, appear poised to significantly increase. The convergence of these two forces is propitious for pathology training. This article examines the opportunities for the use of whole slide images (WSI) in pathology residency training along with the developing potential uses in each of the areas of competency, as categorized by the ACGME. Barriers to WSI adoption in the pathology community are identified along with potentially significant promoters for adoption in training and practice. Current literature and recent presentations are reviewed. Digital pathology coupled with emphasis on competency is a shift of tremendous magnitude that can dramatically improve our abilities to help trainees acquire, demonstrate, and maintain the skills to practice pathology in the generation ahead.
Citation: Journal of Pathology Informatics 2011 2(1):27-27
PubDate: Tue,14 Jun 2011
Issue No: Vol. 2, No. 1 (2011)
- Modified full-field optical coherence tomography: A novel tool for rapid
histology of tissues
Authors: Manu Jain, Nidhi Shukla, Maryem Manzoor, Sylvie Nadolny, Sushmita Mukherjee
Pages: 28 - 28
Abstract: Manu Jain, Nidhi Shukla, Maryem Manzoor, Sylvie Nadolny, Sushmita Mukherjee
Journal of Pathology Informatics 2011 2(1):28-28
Background: Here, we report the first use of a commercial prototype of full-field optical coherence tomography called Light-CT TM . Based on the principle of white light interferometry, Light-CT TM generates quick high-resolution three-dimensional tomographic images from unprocessed tissues. Its advantage over the current intra-surgical diagnostic standard, i.e. frozen section analysis, lies in the absence of freezing artifacts, which allows real-time diagnostic impressions, and/or for the tissues to be triaged for subsequent conventional histopathology. Materials and Methods: In this study, we recapitulate known normal histology in nine formalin fixed ex vivo rat organs (skin, heart, lung, liver, stomach, kidney, prostate, urinary bladder, and testis). Large surface and virtually sectioned stacks of images at varying depths were acquired by a pair of 10x/0.3 numerical aperture water immersion objectives, processed and visualized in real time. Results: Normal histology of the following organs was recapitulated by identifying various tissue microstructures. Skin: epidermis, dermal-epidermal junction and hair follicles with surrounding sebaceous glands in the dermis. Stomach: mucosa with surface pits, submucosa, muscularis propria and serosa. Liver: hepatocytes separated by sinusoidal spaces, central veins and portal triad. Kidney: convoluted tubules, medullary rays (straight tubules) and collecting ducts. Prostate: acini and fibro-muscular stroma. Lung: bronchi, bronchioles, alveolar ducts, alveoli and pleura. Urinary bladder: urothelium, lamina propria, muscularis propria, and serosa. Testis: seminiferous tubules with intra-tubular sperms. Conclusion: Light-CT TM is a powerful imaging tool to perform fast histology on fresh and fixed tissues, without introducing artifacts. Its compact size, ease of handling, fast image acquisition and safe incident light levels makes it well-suited for various intra-operative and intra-procedural triaging and decision making applications.
Citation: Journal of Pathology Informatics 2011 2(1):28-28
PubDate: Tue,14 Jun 2011
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- A data model and database for high-resolution pathology analytical image
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
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
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
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- Implementation of whole slide imaging in surgical pathology: A value added
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- Abstracts: Pathology Informatics 2011 Meeting
Pages: 43 - 43
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
Issue No: Vol. 2, No. 1 (2011)
- High-definition hematoxylin and eosin staining in a transition to digital
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
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
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
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
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
Issue No: Vol. 2, No. 1 (2011)
- Telecytology: Clinical applications, current challenges, and future
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
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
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
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
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
Issue No: Vol. 1, No. 1 (2010)
- Overview of laboratory data tools available in a single electronic medical
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
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
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
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
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
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
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
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
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
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
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 220.127.116.11 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
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
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
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
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
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
Issue No: Vol. 1, No. 1 (2010)
- Abstracts: Pathology Informatics 2010 Meeting
Pages: 18 - 18
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
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
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
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
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
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
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
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
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
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
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
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
Issue No: Vol. 1, No. 1 (2010)