Journal of Pathology Informatics最新文献

{"title":"Fully automatic HER2 tissue segmentation for interpretable HER2 scoring","authors":"Mathias Öttl ,&nbsp;Jana Steenpass ,&nbsp;Frauke Wilm ,&nbsp;Jingna Qiu ,&nbsp;Matthias Rübner ,&nbsp;Corinna Lang-Schwarz ,&nbsp;Cecilia Taverna ,&nbsp;Francesca Tava ,&nbsp;Arndt Hartmann ,&nbsp;Hanna Huebner ,&nbsp;Matthias W. Beckmann ,&nbsp;Peter A. Fasching ,&nbsp;Andreas Maier ,&nbsp;Ramona Erber ,&nbsp;Katharina Breininger","doi":"10.1016/j.jpi.2025.100435","DOIUrl":"10.1016/j.jpi.2025.100435","url":null,"abstract":"<div><div>Breast cancer is the most common cancer in women, with HER2 (human epidermal growth factor receptor 2) overexpression playing a critical role in regulating cell growth and division. HER2 status, assessed according to established scoring guidelines, offers important information for treatment selection. However, the complexity of the task leads to variability in human rater assessments. In this work, we propose a fully automated, interpretable HER2 scoring pipeline based on pixel-level semantic segmentations, designed to align with clinical guidelines. Using polygon annotations, our method balances annotation effort with the ability to capture fine-grained details and larger structures, such as non-invasive tumor tissue.</div><div>To enhance HER2 segmentation, we propose the use of a Wasserstein Dice loss to model class relationships, ensuring robust segmentation and HER2 scoring performance. Additionally, based on observations of pathologists' behavior in clinical practice, we propose a calibration step to the scoring rules, which positively impacts the accuracy and consistency of automated HER2 scoring. Our approach achieves an F1 score of 0.832 on HER2 scoring, demonstrating its effectiveness. This work establishes a potent segmentation pipeline that can be further leveraged to analyze HER2 expression in breast cancer tissue.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100435"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143739022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PIRO: A web-based search platform for pathology reports, leveraging large language models to generate discrete searchable insights","authors":"Scott Robertson ,&nbsp;Venkata Koppireddy ,&nbsp;Jeremy Cumbo ,&nbsp;Hooman Rashidi ,&nbsp;Samer Albahra","doi":"10.1016/j.jpi.2025.100436","DOIUrl":"10.1016/j.jpi.2025.100436","url":null,"abstract":"<div><div>Pathologists rely on access to historical diagnostic case texts for research, education, and peer learning. However, many laboratory information systems (LIS), including Epic Beaker, lack optimized search tools tailored to pathology-specific text queries. To address this need, we developed PIRO (Pathology Information Retrieval Optimizer), a web-based platform enabling efficient text searches of diagnostic archives. Built using FastAPI, Angular, and Apache Solr, PIRO supports both basic and advanced search functionalities, faceted filtering, and data extraction, while ensuring compliance with institutional privacy protocols. PIRO's capabilities extend to case cohort building, search result export, and secure access control within the institutional network. In an 8-month study, we observed significantly higher PIRO adoption rates (67 %) among pathologists compared to Epic Beaker's SlicerDicer (9 %), underscoring PIRO's usability and relevance. Additionally, we implemented a large language model (LLM) to annotate reports with a “Malignancy Risk” label, enhancing search precision and enabling future expansion of automated annotations. Ongoing work focuses on integrating PIRO with our digital pathology platform, enabling direct access to digital slides from case results. PIRO's adaptable design makes it applicable across institutions, advancing search and retrieval efficiency in pathology archives and enhancing support for pathology research and education.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100436"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143746751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fast TILs—A pipeline for efficient TILs estimation in non-small cell Lung cancer","authors":"Nikita Shvetsov ,&nbsp;Anders Sildnes ,&nbsp;Masoud Tafavvoghi ,&nbsp;Lill-Tove Rasmussen Busund ,&nbsp;Stig Manfred Dalen ,&nbsp;Kajsa Møllersen ,&nbsp;Lars Ailo Bongo ,&nbsp;Thomas Karsten Kilvær","doi":"10.1016/j.jpi.2025.100437","DOIUrl":"10.1016/j.jpi.2025.100437","url":null,"abstract":"<div><div>The prognostic relevance of tumor-infiltrating lymphocytes (TILs) in non-small cell Lung cancer (NSCLC) is well-established. However, manual TIL quantification in hematoxylin and eosin (H&amp;E) whole slide images (WSIs) is laborious and prone to variability. To address this, we aim to develop and validate an automated computational pipeline for the quantification of TILs in WSIs of NSCLC. Such a solution in computational pathology can accelerate TIL evaluation, thereby standardizing the prognostication process and facilitating personalized treatment strategies.</div><div>We develop an end-to-end automated pipeline for TIL estimation in Lung cancer WSIs by integrating a patch extraction approach based on hematoxylin component filtering with a machine learning-based patch classification and cell quantification method using the HoVer-Net model architecture. Additionally, we employ randomized patch sampling to further reduce the processed patch amount. We evaluate the effectiveness of the patch sampling procedure, the pipeline's ability to identify informative patches and computational efficiency, and the clinical value of produced scores using patient survival data.</div><div>Our pipeline demonstrates the ability to selectively process informative patches, achieving a balance between computational efficiency and prognostic integrity. The pipeline filtering excludes approximately 70% of all patch candidates. Further, only 5% of eligible patches are necessary to retain the pipeline's prognostic accuracy (c-index = 0.65), resulting in a linear reduction of the total computational time compared to the filtered patch subset analysis. The pipeline's TILs score has a strong association with patient survival and outperforms traditional CD8 immunohistochemical scoring (c-index = 0.59). Kaplan–Meier analysis further substantiates the TILs score's prognostic value.</div><div>This study introduces an automated pipeline for TIL evaluation in Lung cancer WSIs, providing a prognostic tool with potential to improve personalized treatment in NSCLC. The pipeline's computational advances, particularly in reducing processing time, and clinical relevance demonstrate a step forward in computational pathology.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100437"},"PeriodicalIF":0.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143725776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to “After neoadjuvant therapy, axillary sentinel lymph node frozen sections from breast cancer patients are accurately diagnosed using telepathology” [Journal of Pathology Informatics Volume 13, 2022, 100092]","authors":"Valarie McMurtry ,&nbsp;Jane M. Poretta ,&nbsp;Rachel E. Factor","doi":"10.1016/j.jpi.2025.100427","DOIUrl":"10.1016/j.jpi.2025.100427","url":null,"abstract":"","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100427"},"PeriodicalIF":0.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to “Classification of cervical biopsy free-text diagnoses through linear-classifier based natural language processing” [Journal of Pathology Informatics Volume 13, 2022, 100123]","authors":"Jim Wei-Chun Hsu ,&nbsp;Paul Christensen ,&nbsp;Yimin Ge ,&nbsp;S. Wesley Long","doi":"10.1016/j.jpi.2025.100430","DOIUrl":"10.1016/j.jpi.2025.100430","url":null,"abstract":"","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100430"},"PeriodicalIF":0.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to “CNViz: An R/Shiny application for interactive copy number variant visualization in cancer” [Journal of Pathology Informatics Volume 13, 2022, 100089]","authors":"Rebecca G. Ramesh ,&nbsp;Ashkan Bigdeli ,&nbsp;Chase Rushton ,&nbsp;Jason N. Rosenbaum","doi":"10.1016/j.jpi.2025.100431","DOIUrl":"10.1016/j.jpi.2025.100431","url":null,"abstract":"","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100431"},"PeriodicalIF":0.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Custom R Flexdashboard for molecular genetic pathology quality tracking","authors":"Steven Shen ,&nbsp;Ju-Yoon Yoon","doi":"10.1016/j.jpi.2025.100434","DOIUrl":"10.1016/j.jpi.2025.100434","url":null,"abstract":"<div><div>The practice of modern-day laboratory medicine entails extensive, daily practice of tracking various quality metrics of every molecular test to ensure quality maintenance, as well as for laboratory management. While various third-party tools are commercially available, such represent a significant investment for publicly funded institutions. To automate aspects of this quality management, we developed a custom dashboard, written using R. We used R Studio, a freely available software, and employed the <em>Shiny</em> and <em>Flexdashboard</em> packages to develop the code base for the dashboard. Data for the dashboard were pulled from multiple Excel tracking spreadsheets for different clinical assays. The current dashboard allows for dynamic, automated reporting of case volume, and turn-around time, which are regularly reported metrics to CancerCare Ontario for reimbursement purposes. Workload tracking is also made possible, automating calculations regularly performed for billing purposes. The dashboard summarizes various quality metrics for each assay in a single table, viewable by multiple personnel within a single network. Additional features such as filtering quality metrics by date and customization of a variety of plots were also included. Whereas other informatics solutions may be available, our custom solution represents a low-cost system that alleviates a significant workload from various members of the laboratory medicine department, easing the currently significant administrative burden from the “hands-on” staff. Future work will be focused on further improving the accessibility of the dashboard and the integration of additional molecular assays for quality monitoring.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100434"},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GloFinder: AI-empowered QuPath plugin for WSI-level glomerular detection, visualization, and curation","authors":"Jialin Yue ,&nbsp;Tianyuan Yao ,&nbsp;Ruining Deng ,&nbsp;Siqi Lu ,&nbsp;Junlin Guo ,&nbsp;Quan Liu ,&nbsp;Juming Xiong ,&nbsp;Mengmeng Yin ,&nbsp;Haichun Yang ,&nbsp;Yuankai Huo","doi":"10.1016/j.jpi.2025.100433","DOIUrl":"10.1016/j.jpi.2025.100433","url":null,"abstract":"<div><div>Artificial intelligence (AI) has demonstrated significant success in automating the detection of glomeruli—key functional units of the kidney—from whole slide images (WSIs) in kidney pathology. However, existing open-source tools are often distributed as source code or Docker containers, requiring advanced programming skills that hinder accessibility for non-programmers, such as clinicians. Additionally, current models are typically trained on a single dataset and lack flexibility in adjusting confidence levels for predictions. To overcome these challenges, we introduce GloFinder, a QuPath plugin designed for single-click automated glomerular detection across entire WSIs with online editing through the graphical user interface. GloFinder employs CircleNet, an anchor-free detection framework utilizing circle representations for precise object localization, with models trained on approximately 160,000 manually annotated glomeruli. To further enhance accuracy, the plugin incorporates weighted circle fusion—an ensemble method that combines confidence scores from multiple CircleNet models to produce refined predictions, achieving superior performance in glomerular detection. GloFinder enables direct visualization and editing of results in QuPath, facilitating seamless interaction for clinicians and providing a powerful tool for nephropathology research and clinical practice.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100433"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PARAFFIN: A software tool for Pathology Report Automated Feedback for Improved Education of anatomic pathology trainees","authors":"Clarissa E. Jordan,&nbsp;Justin E. Juskewitch,&nbsp;Andrew P. Norgan","doi":"10.1016/j.jpi.2025.100424","DOIUrl":"10.1016/j.jpi.2025.100424","url":null,"abstract":"<div><h3>Background</h3><div>Feedback on the diagnosis and reporting of pathology findings is essential to the training of residents and fellows, but time constraints and other factors can make it difficult to ensure learners are made aware of the outcome of all cases in which they participated. Many trainees attempt to keep track of their cases and later look up final pathology reports in the laboratory information system (LIS); however, this manual and time-consuming process is prone to error and may prevent them from spending time reviewing and learning from these reports.</div></div><div><h3>Methods</h3><div>To address this, we developed a software solution, (<strong>Pa</strong>thology <strong>R</strong>eport <strong>A</strong>utomated <strong>F</strong>eedback <strong>f</strong>or <strong>I</strong>mproved Educatio<strong>n</strong>; “PARAFFIN”), which provides pathology trainees with a weekly email digest containing an attached case log with the date, accession sequence, attending pathologist initials, and final diagnosis text for each case in which they participated. PARAFFIN is implemented as two R scripts running on a Posit Connect server: a data extraction script, which accesses an interactive report from our enterprise analytics SQL server, and a reporting script, which performs recipient-specific filtering and emails the trainee with their personalized case log attached as .txt and .csv files. After implementation, pathology trainees were surveyed about PARAFFIN's impact on report collection and case feedback.</div></div><div><h3>Results</h3><div>Of the total 51 pathology trainees who were receiving PARAFFIN digests at the long-term follow-up timepoint, 20 responded to our survey. 90% (18 of 20) of respondents report that PARAFFIN allows them to spend more time reviewing the content of final anatomic pathology reports, rather than collecting reports. Trainees report utilizing PARAFFIN for feedback on multiple aspects of pathology reporting, with final diagnosis, wording/style of final diagnostic line, and diagnostic comment being most frequently used.</div></div><div><h3>Conclusions</h3><div>Our automated case feedback solution provides trainees with a record of final pathology reports for cases in which they participated, which allows trainees to spend more time reviewing reports for feedback rather than manually collecting them from the LIS.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100424"},"PeriodicalIF":0.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143593458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An international study of stain variability in histopathology using qualitative and quantitative analysis","authors":"Catriona Dunn ,&nbsp;David Brettle ,&nbsp;Chantell Hodgson ,&nbsp;Robert Hughes ,&nbsp;Darren Treanor","doi":"10.1016/j.jpi.2025.100423","DOIUrl":"10.1016/j.jpi.2025.100423","url":null,"abstract":"<div><div>Hematoxylin and eosin (H&amp;E) staining accounts for over 80% of slides stained worldwide. Although routinely used, there are high levels of variation between labs due to different staining methods. Staining is a pivotal part of slide preparation, but quality control is largely subjective, with overall clinical assurance provided by external quality assessment (EQA) services, underpinned by expert assessment. Digital pathology offers the potential to provide objective quantification of stain, through color analysis, to augment EQA assessment.</div><div>This large-scale study evaluated H&amp;E staining in 247 international labs participating in the UK NEQAS CPT EQA programme. Tissue sections were circulated to each lab to stain using their routine H&amp;E staining protocol. The slides were reviewed by independent expert UK NEQAS CPT assessors, and quantitative digital analysis was conducted, comprising of H&amp;E color deconvolution and color difference determination (ΔE).</div><div>Most labs (69%) achieved an EQA score indicating good or excellent staining, with high inter-observer concordance to support this (92.5% within one mark of each other). H&amp;E color difference, ΔE, showed 60% of labs were within 2 ΔE of the mean, which is considered as only perceptible through close observation. There was little correlation found between H&amp;E intensity and assessor score, however, the H&amp;E intensity ratio indicated a trend with assessor score suggesting there may be an optimal stain relationship that should be investigated further.</div><div>The presented hybrid analysis combines expert analysis with objective data. This has the potential to inform upon optimal tissue staining and allows us to consider quantitative standards of H&amp;E staining in pathology practice.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"17 ","pages":"Article 100423"},"PeriodicalIF":0.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}