Pub Date : 2024-12-01DOI: 10.1016/j.jpi.2024.100405
Manon Chossegros , François Delhommeau , Daniel Stockholm , Xavier Tannier
The morphological classification of nucleated blood cells is fundamental for the diagnosis of hematological diseases. Many Deep Learning algorithms have been implemented to automatize this classification task, but most of the time they fail to classify images coming from different sources. This is known as “domain shift”. Whereas some research has been conducted in this area, domain adaptation techniques are often computationally expensive and can introduce significant modifications to initial cell images. In this article, we propose an easy-to-implement workflow where we trained a model to classify images from two datasets, and tested it on images coming from eight other datasets. An EfficientNet model was trained on a source dataset comprising images from two different datasets. It was afterwards fine-tuned on each of the eight target datasets by using 100 or less-annotated images from these datasets. Images from both the source and the target dataset underwent a color transform to put them into a standardized color style. The importance of color transform and fine-tuning was evaluated through an ablation study and visually assessed with scatter plots, and an extensive error analysis was carried out. The model achieved an accuracy higher than 80% for every dataset and exceeded 90% for more than half of the datasets. The presented workflow yielded promising results in terms of generalizability, significantly improving performance on target datasets, whereas keeping low computational cost and maintaining consistent color transformations. Source code is available at: https://github.com/mc2295/WBC_Generalization
{"title":"Improving the generalizability of white blood cell classification with few-shot domain adaptation","authors":"Manon Chossegros , François Delhommeau , Daniel Stockholm , Xavier Tannier","doi":"10.1016/j.jpi.2024.100405","DOIUrl":"10.1016/j.jpi.2024.100405","url":null,"abstract":"<div><div>The morphological classification of nucleated blood cells is fundamental for the diagnosis of hematological diseases. Many Deep Learning algorithms have been implemented to automatize this classification task, but most of the time they fail to classify images coming from different sources. This is known as “domain shift”. Whereas some research has been conducted in this area, domain adaptation techniques are often computationally expensive and can introduce significant modifications to initial cell images. In this article, we propose an easy-to-implement workflow where we trained a model to classify images from two datasets, and tested it on images coming from eight other datasets. An EfficientNet model was trained on a source dataset comprising images from two different datasets. It was afterwards fine-tuned on each of the eight target datasets by using 100 or less-annotated images from these datasets. Images from both the source and the target dataset underwent a color transform to put them into a standardized color style. The importance of color transform and fine-tuning was evaluated through an ablation study and visually assessed with scatter plots, and an extensive error analysis was carried out. The model achieved an accuracy higher than 80% for every dataset and exceeded 90% for more than half of the datasets. The presented workflow yielded promising results in terms of generalizability, significantly improving performance on target datasets, whereas keeping low computational cost and maintaining consistent color transformations. Source code is available at: <span><span>https://github.com/mc2295/WBC_Generalization</span><svg><path></path></svg></span></div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100405"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745793","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}
Pub Date : 2024-11-19DOI: 10.1016/j.jpi.2024.100392
{"title":"Pathology Informatics Summit 2024 Abstracts Ann Arbor Marriott at Eagle Crest Resort May 20-23, 2024 Ann Arbor, Michigan","authors":"","doi":"10.1016/j.jpi.2024.100392","DOIUrl":"10.1016/j.jpi.2024.100392","url":null,"abstract":"","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100392"},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697926","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}
Pub Date : 2024-11-09eCollection Date: 2024-12-01DOI: 10.1016/j.jpi.2024.100407
Silvia Varricchio, Gennaro Ilardi, Daniela Russo, Rosa Maria Di Crescenzo, Angela Crispino, Stefania Staibano, Francesco Merolla
In the current study, we introduced a unique method for identifying and segmenting oral squamous cell carcinoma (OSCC) nuclei, concentrating on those predicted to have significant CAF-1/p60 protein expression. Our suggested model uses the StarDist architecture, a deep-learning framework designed for biomedical image segmentation tasks. The training dataset comprises painstakingly annotated masks created from tissue sections previously stained with hematoxylin and eosin (H&E) and then restained with immunohistochemistry (IHC) for p60 protein. Our algorithm uses subtle morphological and colorimetric H&E cellular characteristics to predict CAF-1/p60 IHC expression in OSCC nuclei. The StarDist-based architecture performs exceptionally well in localizing and segmenting H&E nuclei, previously identified by IHC-based ground truth. In summary, our innovative approach harnesses deep learning and multimodal information to advance the automated analysis of OSCC nuclei exhibiting specific protein expression patterns. This methodology holds promise for expediting accurate pathological assessment and gaining deeper insights into the role of CAF-1/p60 protein within the context of oral cancer progression.
{"title":"Leveraging deep learning for identification and segmentation of \"CAF-1/p60-positive\" nuclei in oral squamous cell carcinoma tissue samples.","authors":"Silvia Varricchio, Gennaro Ilardi, Daniela Russo, Rosa Maria Di Crescenzo, Angela Crispino, Stefania Staibano, Francesco Merolla","doi":"10.1016/j.jpi.2024.100407","DOIUrl":"https://doi.org/10.1016/j.jpi.2024.100407","url":null,"abstract":"<p><p>In the current study, we introduced a unique method for identifying and segmenting oral squamous cell carcinoma (OSCC) nuclei, concentrating on those predicted to have significant CAF-1/p60 protein expression. Our suggested model uses the StarDist architecture, a deep-learning framework designed for biomedical image segmentation tasks. The training dataset comprises painstakingly annotated masks created from tissue sections previously stained with hematoxylin and eosin (H&E) and then restained with immunohistochemistry (IHC) for p60 protein. Our algorithm uses subtle morphological and colorimetric H&E cellular characteristics to predict CAF-1/p60 IHC expression in OSCC nuclei. The StarDist-based architecture performs exceptionally well in localizing and segmenting H&E nuclei, previously identified by IHC-based ground truth. In summary, our innovative approach harnesses deep learning and multimodal information to advance the automated analysis of OSCC nuclei exhibiting specific protein expression patterns. This methodology holds promise for expediting accurate pathological assessment and gaining deeper insights into the role of CAF-1/p60 protein within the context of oral cancer progression.</p>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"100407"},"PeriodicalIF":0.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11653155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855784","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}
Pub Date : 2024-10-28DOI: 10.1016/j.jpi.2024.100404
Marina Aweeda , Carly Fassler , Alexander N. Perez , Alexis Miller , Kavita Prasad , Kayvon F. Sharif , James S. Lewis Jr , Kim A. Ely , Mitra Mehrad , Sarah L. Rohde , Alexander J. Langerman , Kyle Mannion , Robert J. Sinard , James L. Netterville , Eben L. Rosenthal , Michael C. Topf
Background
Positive margins are frequently observed in total laryngectomy (TL) specimens. Effective communication of margin sampling sites and final margin status between surgeons and pathologists is crucial. In this study, we evaluate the utility of multimedia visual pathology reports to facilitate interdisciplinary discussion of margin status in laryngeal cancer surgery.
Methods
Ex vivo laryngeal cancer surgical specimens were three-dimensional (3D) scanned before standard of care pathological analysis. Using computer-aided design software, the 3D model was annotated to reflect inking, sectioning, and margin sampling sites, generating a visual pathology report. These reports were distributed to head and neck surgeons and pathologists postoperatively.
Results
Fifteen laryngeal cancer surgical specimens were 3D scanned and virtually annotated from January 2022 to December 2023. Most specimens (73.3%) were squamous cell carcinomas (SCCs). Among the cases, 26.7% had final positive surgical margins, whereas 13.3% had close margins, defined as <5 mm. The visual pathology report demonstrated sites of close or positive margins on the 3D specimens and was used to facilitate postoperative communication between surgeons and pathologists in 85.7% of these cases. Visual pathology reports were presented in multidisciplinary tumor board discussions (20%), email correspondences (13.3%), and teleconferences (6.7%), and were referenced in the final written pathology reports (26.7%).
Conclusions
3D scanning and virtual annotation of laryngeal cancer specimens for the creation of visual pathology reports is an innovative approach for postoperative pathology documentation, margin analysis, and surgeon–pathologist communication.
{"title":"Visual pathology reports for communication of final margin status in laryngeal cancer surgery","authors":"Marina Aweeda , Carly Fassler , Alexander N. Perez , Alexis Miller , Kavita Prasad , Kayvon F. Sharif , James S. Lewis Jr , Kim A. Ely , Mitra Mehrad , Sarah L. Rohde , Alexander J. Langerman , Kyle Mannion , Robert J. Sinard , James L. Netterville , Eben L. Rosenthal , Michael C. Topf","doi":"10.1016/j.jpi.2024.100404","DOIUrl":"10.1016/j.jpi.2024.100404","url":null,"abstract":"<div><h3>Background</h3><div>Positive margins are frequently observed in total laryngectomy (TL) specimens. Effective communication of margin sampling sites and final margin status between surgeons and pathologists is crucial. In this study, we evaluate the utility of multimedia visual pathology reports to facilitate interdisciplinary discussion of margin status in laryngeal cancer surgery.</div></div><div><h3>Methods</h3><div>Ex vivo laryngeal cancer surgical specimens were three-dimensional (3D) scanned before standard of care pathological analysis. Using computer-aided design software, the 3D model was annotated to reflect inking, sectioning, and margin sampling sites, generating a visual pathology report. These reports were distributed to head and neck surgeons and pathologists postoperatively.</div></div><div><h3>Results</h3><div>Fifteen laryngeal cancer surgical specimens were 3D scanned and virtually annotated from January 2022 to December 2023. Most specimens (73.3%) were squamous cell carcinomas (SCCs). Among the cases, 26.7% had final positive surgical margins, whereas 13.3% had close margins, defined as <5 mm. The visual pathology report demonstrated sites of close or positive margins on the 3D specimens and was used to facilitate postoperative communication between surgeons and pathologists in 85.7% of these cases. Visual pathology reports were presented in multidisciplinary tumor board discussions (20%), email correspondences (13.3%), and teleconferences (6.7%), and were referenced in the final written pathology reports (26.7%).</div></div><div><h3>Conclusions</h3><div>3D scanning and virtual annotation of laryngeal cancer specimens for the creation of visual pathology reports is an innovative approach for postoperative pathology documentation, margin analysis, and surgeon–pathologist communication.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100404"},"PeriodicalIF":0.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697925","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}
Pub Date : 2024-10-23DOI: 10.1016/j.jpi.2024.100402
Nils Englert , Constantin Schwab , Maximilian Legnar , Cleo-Aron Weis
Introduction
Metadata extraction from digitized slides or whole slide image files is a frequent, laborious, and tedious task. In this work, we present a tool to automatically extract all relevant slide information, such as case number, year, slide number, block number, and staining from the macro-images of the scanned slide.
We named the tool Babel fish as it helps translate relevant information printed on the slide. It is written to contain certain basic assumptions regarding, for example, the location of certain information. This can be adapted to the respective location. The extracted metadata can then be used to sort digital slides into databases or to link them with associated case IDs from laboratory information systems.
Material and methods
The tool is based on optical character recognition (OCR). For most information, the easyOCR tool is used. For the block number and cases with insufficient results in the first OCR round, a second OCR with pytesseract is applied.
Two datasets are used: one for tool development has 342 slides; and another for one for testing has 110 slides.
Results
For the testing set, the overall accuracy for retrieving all relevant information per slide is 0.982. Of note, the accuracy for most information parts is 1.000, whereas the accuracy for the block number detection is 0.982.
Conclusion
The Babel fish tool can be used to rename vast amounts of whole slide image files in an image analysis pipeline. Furthermore, it could be an essential part of DICOM conversion pipelines, as it extracts relevant metadata like case number, year, block ID, and staining.
导言:从数字化幻灯片或整个幻灯片图像文件中提取元数据是一项频繁、费力且繁琐的工作。我们将该工具命名为巴别鱼,因为它有助于翻译印在玻片上的相关信息。我们将该工具命名为 "巴别鱼",因为它可以帮助翻译印在幻灯片上的相关信息。它的编写包含了一些基本假设,例如,某些信息的位置。这可以根据相应的位置进行调整。提取的元数据可用于将数字幻灯片分类到数据库中,或将其与实验室信息系统中的相关病例 ID 相链接。对于大多数信息,使用 easyOCR 工具。结果对于测试集,每张幻灯片检索所有相关信息的总体准确率为 0.982。值得注意的是,大多数信息部分的准确率为 1.000,而块号检测的准确率为 0.982。此外,它还可以提取病例号、年份、区块 ID 和染色等相关元数据,是 DICOM 转换管道的重要组成部分。
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Pub Date : 2024-10-20DOI: 10.1016/j.jpi.2024.100403
Martim Afonso , Praphulla M.S. Bhawsar , Monjoy Saha , Jonas S. Almeida , Arlindo L. Oliveira
Whole slide images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to artificial intelligence (AI)-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: (a) accurately predicting the overall cancer phenotype and (b) finding out what cellular morphologies are associated with it at the tile level. To better understand and address these challenges, two existing weakly supervised Multiple Instance Learning (MIL) approaches were explored and compared: Attention MIL (AMIL) and Additive MIL (AdMIL). These architectures were analyzed on tumor detection (a task where these models obtained good results previously) and TP53 mutation detection (a much less explored task). For tumor detection, we built a dataset from Lung Squamous Cell Carcinoma (TCGA-LUSC) slides, with 349 positive and 349 negative slides. The patches were extracted from 5× magnification. For TP53 mutation detection, we explored a dataset built from Invasive Breast Carcinoma (TCGA-BRCA) slides, with 347 positive and 347 negative slides. In this case, we explored three different magnification levels: 5×, 10×, and 20×. Our results show that a modified additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by AMIL (AUC 0.97) on the tumor detection task. TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved. More interestingly from the perspective of the molecular pathologist, we highlight the possible ability of these MIL architectures to identify distinct sensitivities to morphological features (through the detection of regions of interest, ROIs) at different amplification levels. This ability for models to obtain tile-level ROIs is very appealing to pathologists as it provides the possibility for these algorithms to be integrated in a digital staining application for analysis, facilitating the navigation through these high-dimensional images and the diagnostic process.
全玻片图像(WSI)是通过对显微镜玻片进行多尺度高分辨率数字扫描获得的,是现代数字病理学的基石。然而,它们对基于人工智能(AI)/人工智能介导的分析是一个特殊的挑战,因为病理标记通常是在玻片级而不是平片级完成的。医学诊断不仅记录在标本层面,肿瘤基因突变的检测也是通过实验获得的,并由癌症基因组图谱(TCGA)等计划记录在玻片层面。这就构成了双重挑战:(a)准确预测整体癌症表型;(b)在切片层面找出与之相关的细胞形态。为了更好地理解和应对这些挑战,我们探索并比较了两种现有的弱监督多实例学习 (MIL) 方法:注意力 MIL (AMIL) 和添加式 MIL (AdMIL)。我们在肿瘤检测(这些模型之前在这项任务中取得了很好的结果)和 TP53 突变检测(这是一项探索较少的任务)中对这些架构进行了分析。在肿瘤检测方面,我们建立了一个来自肺鳞状细胞癌(TCGA-LUSC)切片的数据集,其中包括 349 张阳性切片和 349 张阴性切片。斑块是从 5 倍放大镜下提取的。在 TP53 突变检测方面,我们利用侵袭性乳腺癌(TCGA-BRCA)切片建立了一个数据集,其中有 347 张阳性切片和 347 张阴性切片。在这种情况下,我们探索了三种不同的放大倍数:5 倍、10 倍和 20 倍。结果表明,在肿瘤检测任务上,MIL 的改进加法实现与参考实现的性能相当(AUC 0.96),仅略高于 AMIL(AUC 0.97)。TP53 突变对细胞形态解析度较高的应用特征最为敏感。从分子病理学家的角度来看,更有趣的是,我们强调了这些 MIL 架构在不同扩增水平下识别形态特征(通过检测感兴趣区,ROI)的不同敏感性的可能能力。模型获得瓦片级 ROI 的这种能力对病理学家来说非常有吸引力,因为它提供了将这些算法集成到数字染色应用中进行分析的可能性,从而为浏览这些高维图像和诊断过程提供了便利。
{"title":"Multiple Instance Learning for WSI: A comparative analysis of attention-based approaches","authors":"Martim Afonso , Praphulla M.S. Bhawsar , Monjoy Saha , Jonas S. Almeida , Arlindo L. Oliveira","doi":"10.1016/j.jpi.2024.100403","DOIUrl":"10.1016/j.jpi.2024.100403","url":null,"abstract":"<div><div>Whole slide images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to artificial intelligence (AI)-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: (a) accurately predicting the overall cancer phenotype and (b) finding out what cellular morphologies are associated with it at the tile level. To better understand and address these challenges, two existing weakly supervised Multiple Instance Learning (MIL) approaches were explored and compared: Attention MIL (AMIL) and Additive MIL (AdMIL). These architectures were analyzed on tumor detection (a task where these models obtained good results previously) and TP53 mutation detection (a much less explored task). For tumor detection, we built a dataset from Lung Squamous Cell Carcinoma (TCGA-LUSC) slides, with 349 positive and 349 negative slides. The patches were extracted from 5× magnification. For TP53 mutation detection, we explored a dataset built from Invasive Breast Carcinoma (TCGA-BRCA) slides, with 347 positive and 347 negative slides. In this case, we explored three different magnification levels: 5×, 10×, and 20×. Our results show that a modified additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by AMIL (AUC 0.97) on the tumor detection task. TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved. More interestingly from the perspective of the molecular pathologist, we highlight the possible ability of these MIL architectures to identify distinct sensitivities to morphological features (through the detection of regions of interest, ROIs) at different amplification levels. This ability for models to obtain tile-level ROIs is very appealing to pathologists as it provides the possibility for these algorithms to be integrated in a digital staining application for analysis, facilitating the navigation through these high-dimensional images and the diagnostic process.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100403"},"PeriodicalIF":0.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652433","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}
Pub Date : 2024-10-09DOI: 10.1016/j.jpi.2024.100401
Thomas W. Bauer , Matthew G. Hanna , Kelly D. Smith , S. Joseph Sirintrapun , Meera R. Hameed , Deepti Reddi , Bernard S. Chang , Orly Ardon , Xiaozhi Zhou , Jenny V. Lewis , Shubham Dayal , Joseph Chiweshe , David Ferber , Aysegul Ergin Sutcu , Michael White
Background
Digital pathology systems (DPS) are emerging as capable technologies for clinical practice. Studies have analyzed pathologists' diagnostic concordance by comparing reviews of whole slide images (WSIs) to glass slides (e.g., accuracy). This observational study evaluated the reproducibility of pathologists' diagnostic reviews using the Aperio GT 450 DX under slightly different conditions (precision).
Method
Diagnostic precision was tested in three conditions: intra-system (within systems), inter-system/site (between systems/sites), and intra- and inter-pathologist (within and between pathologists). A total of five study/reading pathologists (one pathologist each for intra-system, inter-system/site, and three for intra-pathologist/inter-pathologist analyses) were assigned to the respective sub-studies.
A panel of 69 glass slides with 23 unique histological features was used to evaluate the WSI system's precision. Each glass slide was scanned to generate a unique WSI. From each WSI, the field of view (FOV) was generated (at least 2 FOVs/WSI), which included the selected features (1–3 features/FOV). Each pathologist reviewed the digital slides and identified which morphological features, if any, were present in each defined FOV. To minimize recall bias, an additional 12 wild card slides from different organ types were used for which FOVs were extracted. The pathologists also read these wild card slides FOVs; however, the corresponding feature identification was not included in the final data analysis.
Results
Each measured endpoint met the pre-defined acceptance criteria of the lower bound of the 95% confidence interval (CI) overall agreement (OA) rate being ≥85% for each sub-study. The lower bound of the 95% CI for the intra-system OA rate was 95.8%; for inter-system analysis, it was 94.9%; for intra-pathologist analysis, 92.4%, whereas for inter-pathologist analyses, the lower bound of the 95% CI of the OA was 90.6%.
Conclusion
The study results indicate that pathologists using the Aperio GT 450 DX WSI system can precisely identify histological features that may be required for accurately diagnosing anatomic pathology cases.
背景数字病理系统(DPS)正在成为临床实践的有效技术。有研究通过比较全切片图像(WSI)和玻璃切片的审查结果(如准确性)来分析病理学家的诊断一致性。本观察性研究评估了病理学家在略有不同的条件下使用 Aperio GT 450 DX 进行诊断审查的可重复性(精确性)。方法在三种条件下测试了诊断精确性:系统内(系统内部)、系统间/站点间(系统/站点之间)以及病理学家内部和病理学家之间(病理学家内部和病理学家之间)。共有五名研究/阅片病理学家(系统内、系统间/病理点各一名,病理学家内/病理学家间分析各三名)被分配到相应的子研究中。对每张玻璃玻片进行扫描,生成唯一的 WSI。从每个 WSI 生成视场(FOV)(至少 2 个 FOV/WSI),其中包括选定的特征(1-3 个特征/FOV)。每位病理学家查看数字切片,确定每个定义的视场(FOV)中存在哪些形态特征(如果有的话)。为了尽量减少回忆偏差,病理学家还使用了另外 12 张来自不同器官类型的通配切片来提取 FOV。结果每一项测量终点均符合预先设定的接受标准,即每项子研究的95%置信区间(CI)总体一致性(OA)率下限≥85%。系统内 OA 率的 95% CI 下限为 95.8%;系统间分析的 OA 率为 94.9%;病理学家内部分析的 OA 率为 92.4%,而病理学家间分析的 OA 率的 95% CI 下限为 90.6%。
{"title":"A multicenter study to evaluate the analytical precision by pathologists using the Aperio GT 450 DX","authors":"Thomas W. Bauer , Matthew G. Hanna , Kelly D. Smith , S. Joseph Sirintrapun , Meera R. Hameed , Deepti Reddi , Bernard S. Chang , Orly Ardon , Xiaozhi Zhou , Jenny V. Lewis , Shubham Dayal , Joseph Chiweshe , David Ferber , Aysegul Ergin Sutcu , Michael White","doi":"10.1016/j.jpi.2024.100401","DOIUrl":"10.1016/j.jpi.2024.100401","url":null,"abstract":"<div><h3>Background</h3><div>Digital pathology systems (DPS) are emerging as capable technologies for clinical practice. Studies have analyzed pathologists' diagnostic concordance by comparing reviews of whole slide images (WSIs) to glass slides (e.g., accuracy). This observational study evaluated the reproducibility of pathologists' diagnostic reviews using the Aperio GT 450 DX under slightly different conditions (precision).</div></div><div><h3>Method</h3><div>Diagnostic precision was tested in three conditions: intra-system (within systems), inter-system/site (between systems/sites), and intra- and inter-pathologist (within and between pathologists). A total of five study/reading pathologists (one pathologist each for intra-system, inter-system/site, and three for intra-pathologist/inter-pathologist analyses) were assigned to the respective sub-studies.</div><div>A panel of 69 glass slides with 23 unique histological features was used to evaluate the WSI system's precision. Each glass slide was scanned to generate a unique WSI. From each WSI, the field of view (FOV) was generated (at least 2 FOVs/WSI), which included the selected features (1–3 features/FOV). Each pathologist reviewed the digital slides and identified which morphological features, if any, were present in each defined FOV. To minimize recall bias, an additional 12 wild card slides from different organ types were used for which FOVs were extracted. The pathologists also read these wild card slides FOVs; however, the corresponding feature identification was not included in the final data analysis.</div></div><div><h3>Results</h3><div>Each measured endpoint met the pre-defined acceptance criteria of the lower bound of the 95% confidence interval (CI) overall agreement (OA) rate being ≥85% for each sub-study. The lower bound of the 95% CI for the intra-system OA rate was 95.8%; for inter-system analysis, it was 94.9%; for intra-pathologist analysis, 92.4%, whereas for inter-pathologist analyses, the lower bound of the 95% CI of the OA was 90.6%.</div></div><div><h3>Conclusion</h3><div>The study results indicate that pathologists using the Aperio GT 450 DX WSI system can precisely identify histological features that may be required for accurately diagnosing anatomic pathology cases.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100401"},"PeriodicalIF":0.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652531","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}
Pub Date : 2024-09-30DOI: 10.1016/j.jpi.2024.100400
Enzo Gallo , Davide Guardiani , Martina Betti , Brindusa Ana Maria Arteni , Simona Di Martino , Sara Baldinelli , Theodora Daralioti , Elisabetta Merenda , Andrea Ascione , Paolo Visca , Edoardo Pescarmona , Marialuisa Lavitrano , Paola Nisticò , Gennaro Ciliberto , Matteo Pallocca
Purpose
The abundance and distribution of tumor-infiltrating lymphocytes (TILs) as well as that of other components of the tumor microenvironment is of particular importance for predicting response to immunotherapy in lung cancer (LC). We describe here a pilot study employing artificial intelligence (AI) in the assessment of TILs and other cell populations, intending to reduce the inter- or intra-observer variability that commonly characterizes this evaluation.
Design
We developed a machine learning-based classifier to detect tumor, immune, and stromal cells on hematoxylin and eosin-stained sections, using the open-source framework QuPath. We evaluated the quantity of the aforementioned three cell populations among 37 LC whole slide images regions of interest, comparing the assessments made by five pathologists, both before and after using graphical predictions made by AI, for a total of 1110 quantitative measurements.
Results
Our findings indicate noteworthy variations in score distribution among pathologists and between individual pathologists and AI. The AI-guided pathologist's evaluations resulted in reduction of significant discrepancies across pathologists: three comparisons showed a loss of significance (p > 0.05), whereas other four showed a reduction in significance (p > 0.01).
Conclusions
We show that employing a machine learning approach in cell population quantification reduces inter- and intra-observer variability, improving reproducibility and facilitating its use in further validation studies.
{"title":"AI drives the assessment of lung cancer microenvironment composition","authors":"Enzo Gallo , Davide Guardiani , Martina Betti , Brindusa Ana Maria Arteni , Simona Di Martino , Sara Baldinelli , Theodora Daralioti , Elisabetta Merenda , Andrea Ascione , Paolo Visca , Edoardo Pescarmona , Marialuisa Lavitrano , Paola Nisticò , Gennaro Ciliberto , Matteo Pallocca","doi":"10.1016/j.jpi.2024.100400","DOIUrl":"10.1016/j.jpi.2024.100400","url":null,"abstract":"<div><h3>Purpose</h3><div>The abundance and distribution of tumor-infiltrating lymphocytes (TILs) as well as that of other components of the tumor microenvironment is of particular importance for predicting response to immunotherapy in lung cancer (LC). We describe here a pilot study employing artificial intelligence (AI) in the assessment of TILs and other cell populations, intending to reduce the inter- or intra-observer variability that commonly characterizes this evaluation.</div></div><div><h3>Design</h3><div>We developed a machine learning-based classifier to detect tumor, immune, and stromal cells on hematoxylin and eosin-stained sections, using the open-source framework <em>QuPath</em>. We evaluated the quantity of the aforementioned three cell populations among 37 LC whole slide images regions of interest, comparing the assessments made by five pathologists, both before and after using graphical predictions made by AI, for a total of 1110 quantitative measurements.</div></div><div><h3>Results</h3><div>Our findings indicate noteworthy variations in score distribution among pathologists and between individual pathologists and AI. The AI-guided pathologist's evaluations resulted in reduction of significant discrepancies across pathologists: three comparisons showed a loss of significance (<em>p</em> > 0.05), whereas other four showed a reduction in significance (<em>p</em> > 0.01).</div></div><div><h3>Conclusions</h3><div>We show that employing a machine learning approach in cell population quantification reduces inter- and intra-observer variability, improving reproducibility and facilitating its use in further validation studies.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100400"},"PeriodicalIF":0.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523282","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}
Pub Date : 2024-09-28DOI: 10.1016/j.jpi.2024.100399
Carly Fassler , Marina Aweeda , Alexander N. Perez , Yuna Chung , Spencer Yueh , Robert J. Sinard , Sarah L. Rohde , Kyle Mannion , Alexander J. Langerman , Eben L. Rosenthal , Jie Ying Wu , Mitra Mehrad , Kim Ely , James S. Lewis Jr , Michael C. Topf
Background
The current standard-of-care pathology report relies only on lengthy written text descriptions without a visual representation of the resected cancer specimen. This study demonstrates the feasibility of incorporating virtual, three-dimensional (3D) visual pathology reports to improve communication of final pathology reporting.
Materials and methods
Surgical specimens are 3D scanned and virtually mapped alongside the pathology team to replicate grossing. The 3D specimen maps are incorporated into a hybrid visual pathology report which displays the resected specimen and sampled margins alongside gross measurements, tumor characteristics, and microscopic diagnoses.
Results
Visual pathology reports were created for 10 head and neck cancer cases. Each report concisely communicated information from the final pathology report in a single page and contained significantly fewer words (293.4 words) than standard written pathology reports (850.1 words, p < 0.01).
Conclusions
We establish the feasibility of a novel visual pathology report that includes an annotated visual model of the resected cancer specimen in place of lengthy written text of standard of care head and neck cancer pathology reports.
{"title":"Digital mapping of resected cancer specimens: The visual pathology report","authors":"Carly Fassler , Marina Aweeda , Alexander N. Perez , Yuna Chung , Spencer Yueh , Robert J. Sinard , Sarah L. Rohde , Kyle Mannion , Alexander J. Langerman , Eben L. Rosenthal , Jie Ying Wu , Mitra Mehrad , Kim Ely , James S. Lewis Jr , Michael C. Topf","doi":"10.1016/j.jpi.2024.100399","DOIUrl":"10.1016/j.jpi.2024.100399","url":null,"abstract":"<div><h3>Background</h3><div>The current standard-of-care pathology report relies only on lengthy written text descriptions without a visual representation of the resected cancer specimen. This study demonstrates the feasibility of incorporating virtual, three-dimensional (3D) visual pathology reports to improve communication of final pathology reporting.</div></div><div><h3>Materials and methods</h3><div>Surgical specimens are 3D scanned and virtually mapped alongside the pathology team to replicate grossing. The 3D specimen maps are incorporated into a hybrid visual pathology report which displays the resected specimen and sampled margins alongside gross measurements, tumor characteristics, and microscopic diagnoses.</div></div><div><h3>Results</h3><div>Visual pathology reports were created for 10 head and neck cancer cases. Each report concisely communicated information from the final pathology report in a single page and contained significantly fewer words (293.4 words) than standard written pathology reports (850.1 words, <em>p</em> < 0.01).</div></div><div><h3>Conclusions</h3><div>We establish the feasibility of a novel visual pathology report that includes an annotated visual model of the resected cancer specimen in place of lengthy written text of standard of care head and neck cancer pathology reports.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100399"},"PeriodicalIF":0.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432514","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}
Pub Date : 2024-09-26DOI: 10.1016/j.jpi.2024.100398
Rashiduzzaman Shakil, Sadia Islam, Bonna Akter
Cervical cancer is a cancer that remains a significant global health challenge all over the world. Due to improper screening in the early stages, and healthcare disparities, a large number of women are suffering from this disease, and the mortality rate increases day by day. Hence, in these studies, we presented a precise approach utilizing six different machine learning models (decision tree, logistic regression, naïve bayes, random forest, k nearest neighbors, support vector machine), which can predict the early stage of cervical cancer by analysing 36 risk factor attributes of 858 individuals. In addition, two data balancing techniques—Synthetic Minority Oversampling Technique and Adaptive Synthetic Sampling—were used to mitigate the data imbalance issues. Furthermore, Chi-square and Least Absolute Shrinkage and Selection Operator are two distinct feature selection processes that have been applied to evaluate the feature rank, which are mostly correlated to identify the particular disease, and also integrate an explainable artificial intelligence technique, namely Shapley Additive Explanations, for clarifying the model outcome. The applied machine learning model outcome is evaluated by performance evaluation matrices, namely accuracy, sensitivity, specificity, precision, f1-score, false-positive rate and false-negative rate, and area under the Receiver operating characteristic curve score. The decision tree outperformed in Chi-square feature selection with outstanding accuracy with 97.60%, 98.73% sensitivity, 80% specificity, and 98.73% precision, respectively. During the data imbalance, DT performed 97% accuracy, 99.35% sensitivity, 69.23% specificity, and 97.45% precision. This research is focused on developing diagnostic frameworks with automated tools to improve the detection and management of cervical cancer, as well as on helping healthcare professionals deliver more efficient and personalized care to their patients.
{"title":"A precise machine learning model: Detecting cervical cancer using feature selection and explainable AI","authors":"Rashiduzzaman Shakil, Sadia Islam, Bonna Akter","doi":"10.1016/j.jpi.2024.100398","DOIUrl":"10.1016/j.jpi.2024.100398","url":null,"abstract":"<div><div>Cervical cancer is a cancer that remains a significant global health challenge all over the world. Due to improper screening in the early stages, and healthcare disparities, a large number of women are suffering from this disease, and the mortality rate increases day by day. Hence, in these studies, we presented a precise approach utilizing six different machine learning models (decision tree, logistic regression, naïve bayes, random forest, k nearest neighbors, support vector machine), which can predict the early stage of cervical cancer by analysing 36 risk factor attributes of 858 individuals. In addition, two data balancing techniques—Synthetic Minority Oversampling Technique and Adaptive Synthetic Sampling—were used to mitigate the data imbalance issues. Furthermore, Chi-square and Least Absolute Shrinkage and Selection Operator are two distinct feature selection processes that have been applied to evaluate the feature rank, which are mostly correlated to identify the particular disease, and also integrate an explainable artificial intelligence technique, namely Shapley Additive Explanations, for clarifying the model outcome. The applied machine learning model outcome is evaluated by performance evaluation matrices, namely accuracy, sensitivity, specificity, precision, f1-score, false-positive rate and false-negative rate, and area under the Receiver operating characteristic curve score. The decision tree outperformed in Chi-square feature selection with outstanding accuracy with 97.60%, 98.73% sensitivity, 80% specificity, and 98.73% precision, respectively. During the data imbalance, DT performed 97% accuracy, 99.35% sensitivity, 69.23% specificity, and 97.45% precision. This research is focused on developing diagnostic frameworks with automated tools to improve the detection and management of cervical cancer, as well as on helping healthcare professionals deliver more efficient and personalized care to their patients.</div></div>","PeriodicalId":37769,"journal":{"name":"Journal of Pathology Informatics","volume":"15 ","pages":"Article 100398"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442480","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}