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Journal of Pathology Informatics

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https://www.readbyqxmd.com/read/28066684/pathology-report-data-extraction-from-relational-database-using-r-with-extraction-from-reports-on-melanoma-of-skin-as-an-example
#1
Jay J Ye
BACKGROUND: Different methods have been described for data extraction from pathology reports with varying degrees of success. Here a technique for directly extracting data from relational database is described. METHODS: Our department uses synoptic reports modified from College of American Pathologists (CAP) Cancer Protocol Templates to report most of our cancer diagnoses. Choosing the melanoma of skin synoptic report as an example, R scripting language extended with RODBC package was used to query the pathology information system database...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28066683/computer-based-image-analysis-in-breast-pathology
#2
REVIEW
Ziba Gandomkar, Patrick C Brennan, Claudia Mello-Thoms
Whole slide imaging (WSI) has the potential to be utilized in telepathology, teleconsultation, quality assurance, clinical education, and digital image analysis to aid pathologists. In this paper, the potential added benefits of computer-assisted image analysis in breast pathology are reviewed and discussed. One of the major advantages of WSI systems is the possibility of doing computer-based image analysis on the digital slides. The purpose of computer-assisted analysis of breast virtual slides can be (i) segmentation of desired regions or objects such as diagnostically relevant areas, epithelial nuclei, lymphocyte cells, tubules, and mitotic figures, (ii) classification of breast slides based on breast cancer (BCa) grades, the invasive potential of tumors, or cancer subtypes, (iii) prognosis of BCa, or (iv) immunohistochemical quantification...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28066682/detecting-and-segmenting-cell-nuclei-in-two-dimensional-microscopy-images
#3
Chi Liu, Fei Shang, John A Ozolek, Gustavo K Rohde
INTRODUCTION: Cell nuclei are important indicators of cellular processes and diseases. Segmentation is an essential stage in systems for quantitative analysis of nuclei extracted from microscopy images. Given the wide variety of nuclei appearance in different organs and staining procedures, a plethora of methods have been described in the literature to improve the segmentation accuracy and robustness. MATERIALS AND METHODS: In this paper, we propose an unsupervised method for cell nuclei detection and segmentation in two-dimensional microscopy images...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994941/a-multisite-validation-of-whole-slide-imaging-for-primary-diagnosis-using-standardized-data-collection-and-analysis
#4
Katy Wack, Laura Drogowski, Murray Treloar, Andrew Evans, Jonhan Ho, Anil Parwani, Michael C Montalto
CONTEXT: Text-based reporting and manual arbitration for whole slide imaging (WSI) validation studies are labor intensive and do not allow for consistent, scalable, and repeatable data collection or analysis. OBJECTIVE: The objective of this study was to establish a method of data capture and analysis using standardized codified checklists and predetermined synoptic discordance tables and to use these methods in a pilot multisite validation study. METHODS AND STUDY DESIGN: Fifteen case report form checklists were generated from the College of American Pathology cancer protocols...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994940/reflex-test-reminders-in-required-cancer-synoptic-templates-decrease-order-entry-error-an-analysis-of-mismatch-repair-immunohistochemical-orders-to-screen-for-lynch-syndrome
#5
Mark R Kilgore, Carrie A McIlwain, Rodney A Schmidt, Barbara M Norquist, Elizabeth M Swisher, Rochelle L Garcia, Mara H Rendi
BACKGROUND: Endometrial carcinoma (EC) is the most common extracolonic malignant neoplasm associated with Lynch syndrome (LS). LS is caused by autosomal dominant germline mutations in DNA mismatch repair (MMR) genes. Screening for LS in EC is often evaluated by loss of immunohistochemical (IHC) expression of DNA MMR enzymes MLH1, MSH2, MSH6, and PMS2 (MMR IHC). In July 2013, our clinicians asked that we screen all EC in patients ≤60 for loss of MMR IHC expression. Despite this policy, several cases were not screened or screening was delayed...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994939/pointwise-mutual-information-quantifies-intratumor-heterogeneity-in-tissue-sections-labeled-with-multiple-fluorescent-biomarkers
#6
Daniel M Spagnolo, Rekha Gyanchandani, Yousef Al-Kofahi, Andrew M Stern, Timothy R Lezon, Albert Gough, Dan E Meyer, Fiona Ginty, Brion Sarachan, Jeffrey Fine, Adrian V Lee, D Lansing Taylor, S Chakra Chennubhotla
BACKGROUND: Measures of spatial intratumor heterogeneity are potentially important diagnostic biomarkers for cancer progression, proliferation, and response to therapy. Spatial relationships among cells including cancer and stromal cells in the tumor microenvironment (TME) are key contributors to heterogeneity. METHODS: We demonstrate how to quantify spatial heterogeneity from immunofluorescence pathology samples, using a set of 3 basic breast cancer biomarkers as a test case...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994938/the-utility-of-including-pathology-reports-in-improving-the-computational-identification-of-patients
#7
Wei Chen, Yungui Huang, Brendan Boyle, Simon Lin
BACKGROUND: Celiac disease (CD) is a common autoimmune disorder. Efficient identification of patients may improve chronic management of the disease. Prior studies have shown searching International Classification of Diseases-9 (ICD-9) codes alone is inaccurate for identifying patients with CD. In this study, we developed automated classification algorithms leveraging pathology reports and other clinical data in Electronic Health Records (EHRs) to refine the subset population preselected using ICD-9 code (579...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994937/the-growing-need-for-microservices-in-bioinformatics
#8
Christopher L Williams, Jeffrey C Sica, Robert T Killen, Ulysses G J Balis
OBJECTIVE: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27761297/erratum-antibody-supervised-deep-learning-for-quantification-of-tumor-infiltrating-immune-cells-in-hematoxylin-and-eosin-stained-breast-cancer-samples
#9
(no author information available yet)
[This corrects the article on p. 38 in vol. 7, PMID: 27688929.].
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688931/rates-of-provision-of-clinical-information-in-the-skin-biopsy-requisition-form-and-corresponding-encounter-visit-note
#10
Meredith A Olson, Christine M Lohse, Nneka I Comfere
BACKGROUND: The skin biopsy requisition form (RF) serves as a key communication tool for transfer of relevant information related to skin biopsy between clinicians and pathologists. Clinical information in the skin biopsy RF is frequently missing or incomplete. OBJECTIVE: To determine the rates of provision of critical clinical information necessary for histopathologic interpretation in the skin biopsy RF and encounter visit note (EVN). METHODS: A retrospective review of 300 RFs and corresponding EVNs from May 1 to 7, 2012, in a tertiary care dermatology practice...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688930/a-novel-leadership-fellowship-in-digital-pathology
#11
Bethany Jill Williams, Darren Treanor
No abstract text is available yet for this article.
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688929/antibody-supervised-deep-learning-for-quantification-of-tumor-infiltrating-immune-cells-in-hematoxylin-and-eosin-stained-breast-cancer-samples
#12
Riku Turkki, Nina Linder, Panu E Kovanen, Teijo Pellinen, Johan Lundin
BACKGROUND: Immune cell infiltration in tumor is an emerging prognostic biomarker in breast cancer. The gold standard for quantification of immune cells in tissue sections is visual assessment through a microscope, which is subjective and semi-quantitative. In this study, we propose and evaluate an approach based on antibody-guided annotation and deep learning to quantify immune cell-rich areas in hematoxylin and eosin (H&E) stained samples. METHODS: Consecutive sections of formalin-fixed parafin-embedded samples obtained from the primary tumor of twenty breast cancer patients were cut and stained with H&E and the pan-leukocyte CD45 antibody...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688928/experience-of-maintaining-laboratory-educational-website-s-sustainability
#13
Izak B Dimenstein
Laboratory methodology websites are specialized niche websites. The visibility of a niche website transforms it into an authority site on a particular "niche of knowledge." This article presents some ways in which a laboratory methodology website can maintain its sustainability. The optimal composition of the website includes a basic content, a blog, and an ancillary part. This article discusses experimenting with the search engine optimization query results page. Strategic placement of keywords and even phrases, as well as fragmentation of the post's material, can improve the website's visibility to search engines...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688927/a-novel-method-for-morphological-pleomorphism-and-heterogeneity-quantitative-measurement-named-cell-feature-level-co-occurrence-matrix
#14
Akira Saito, Yasushi Numata, Takuya Hamada, Tomoyoshi Horisawa, Eric Cosatto, Hans-Peter Graf, Masahiko Kuroda, Yoichiro Yamamoto
BACKGROUND: Recent developments in molecular pathology and genetic/epigenetic analysis of cancer tissue have resulted in a marked increase in objective and measurable data. In comparison, the traditional morphological analysis approach to pathology diagnosis, which can connect these molecular data and clinical diagnosis, is still mostly subjective. Even though the advent and popularization of digital pathology has provided a boost to computer-aided diagnosis, some important pathological concepts still remain largely non-quantitative and their associated data measurements depend on the pathologist's sense and experience...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688926/the-coming-paradigm-shift-a-transition-from-manual-to-automated-microscopy
#15
EDITORIAL
Navid Farahani, Corey E Monteith
The field of pathology has used light microscopy (LM) extensively since the mid-19(th) century for examination of histological tissue preparations. This technology has remained the foremost tool in use by pathologists even as other fields have undergone a great change in recent years through new technologies. However, as new microscopy techniques are perfected and made available, this reliance on the standard LM will likely begin to change. Advanced imaging involving both diffraction-limited and subdiffraction techniques are bringing nondestructive, high-resolution, molecular-level imaging to pathology...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27563491/improving-the-creation-and-reporting-of-structured-findings-during-digital-pathology-review
#16
Ida Cervin, Jesper Molin, Claes Lundström
BACKGROUND: Today, pathology reporting consists of many separate tasks, carried out by multiple people. Common tasks include dictation during case review, transcription, verification of the transcription, report distribution, and report the key findings to follow-up registries. Introduction of digital workstations makes it possible to remove some of these tasks and simplify others. This study describes the work presented at the Nordic Symposium on Digital Pathology 2015, in Linköping, Sweden...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27563490/nder-a-novel-web-application-using-annotated-whole-slide-images-for-rapid-improvements-in-human-pattern-recognition
#17
Nicholas P Reder, Daniel Glasser, Suzanne M Dintzis, Mara H Rendi, Rochelle L Garcia, Jonathan C Henriksen, Mark R Kilgore
CONTEXT: Whole-slide images (WSIs) present a rich source of information for education, training, and quality assurance. However, they are often used in a fashion similar to glass slides rather than in novel ways that leverage the advantages of WSI. We have created a pipeline to transform annotated WSI into pattern recognition training, and quality assurance web application called novel diagnostic electronic resource (NDER). AIMS: Create an efficient workflow for extracting annotated WSI for use by NDER, an attractive web application that provides high-throughput training...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27563489/comparing-whole-slide-digital-images-versus-traditional-glass-slides-in-the-detection-of-common-microscopic-features-seen-in-dermatitis
#18
Nikki S Vyas, Michael Markow, Carlos Prieto-Granada, Sudeep Gaudi, Leslie Turner, Paul Rodriguez-Waitkus, Jane L Messina, Drazen M Jukic
BACKGROUND: The quality and limitations of digital slides are not fully known. We aimed to estimate intrapathologist discrepancy in detecting specific microscopic features on glass slides and digital slides created by scanning at ×20. METHODS: Hematoxylin and eosin and periodic acid-Schiff glass slides were digitized using the Mirax Scan (Carl Zeiss Inc., Germany). Six pathologists assessed 50-71 digital slides. We recorded objective magnification, total time, and detection of the following: Mast cells; eosinophils; plasma cells; pigmented macrophages; melanin in the epidermis; fungal bodies; neutrophils; civatte bodies; parakeratosis; and sebocytes...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27563488/deep-learning-for-digital-pathology-image-analysis-a-comprehensive-tutorial-with-selected-use-cases
#19
Andrew Janowczyk, Anant Madabhushi
BACKGROUND: Deep learning (DL) is a representation learning approach ideally suited for image analysis challenges in digital pathology (DP). The variety of image analysis tasks in the context of DP includes detection and counting (e.g., mitotic events), segmentation (e.g., nuclei), and tissue classification (e.g., cancerous vs. non-cancerous). Unfortunately, issues with slide preparation, variations in staining and scanning across sites, and vendor platforms, as well as biological variance, such as the presentation of different grades of disease, make these image analysis tasks particularly challenging...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27563487/clinically-inspired-automatic-classification-of-ovarian-carcinoma-subtypes
#20
Aïcha BenTaieb, Masoud S Nosrati, Hector Li-Chang, David Huntsman, Ghassan Hamarneh
CONTEXT: It has been shown that ovarian carcinoma subtypes are distinct pathologic entities with differing prognostic and therapeutic implications. Histotyping by pathologists has good reproducibility, but occasional cases are challenging and require immunohistochemistry and subspecialty consultation. Motivated by the need for more accurate and reproducible diagnoses and to facilitate pathologists' workflow, we propose an automatic framework for ovarian carcinoma classification. MATERIALS AND METHODS: Our method is inspired by pathologists' workflow...
2016: Journal of Pathology Informatics
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