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MuCoSA: Multi-contextual similarity assessment for histopathology image search 粘膜:组织病理学图像搜索的多上下文相似性评估
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100533
Gyu Yeong Kim , Yongjun Jeon , Hoyeon Jeong , Seungkyun Lee , Hyungbin Kim , Boram Lee , Kyu-Hwan Jung , David Joon Ho , Yoon-La Choi
Histological diagnosis in pathology often begins with visual identification of morphological patterns that resemble known disease entities. Whereas digital pathology and augmented intelligence have enabled reverse image search in histopathology, most existing frameworks rely on single-magnification image patches and slide-level labels, limiting their ability to capture tissue morphologies with at various levels of granularity and scale. To address this, we propose Progressive Regional Image Sequence by Magnification (PRISM), a sequence of images that captures contextual information across multiple magnifications. Building on this, we introduce Multi-Contextual Similarity Assessment (MuCoSA), a PRISM-based image retrieval framework that leverages pre-trained feature encoders without additional fine-tuning. To evaluate MuCoSA's performance, we constructed reference and query PRISM datasets utilizing histological patterns of lung adenocarcinoma. Whole-slide image (WSIs) from Samsung Medical Center were used as reference and internal query, whereas those from The Cancer Genome Atlas served as external query. For each WSI, representative regions of interest were selected and converted into PRISM structure. Similarity between two PRISMs was calculated by averaging the cosine similarities of corresponding patches at the same magnification level across all magnifications. We conducted a comprehensive evaluation across different feature encoders, magnification levels, receptive field sizes, and both internal/external query conditions. As a result, MuCoSA with a multi-magnification outperformed single-magnification methods. For instance, MuCoSA using UNI2-h encoder with eight magnifications achieved an F1-score of 0.8051 (95% CI: 0.7843–0.8267), mAP@5 of 0.7065 (95% CI: 0.6893–0.7250), and mMV@5 of 0.8232 (95% CI: 0.8038–0.8434), all significantly higher than the single-magnification baseline (p < 0.0001). Furthermore, confusion matrices and visual inspection confirmed that search results were closely aligned with the morphological perceptions of pathologists. In conclusion, our study demonstrates that using a simple and efficient framework like MuCoSA with multi-magnification PRISM without fine-tuning can significantly improve image search in histopathology. We anticipate that MuCoSA can assist pathologists in making more accurate and consistent diagnoses, thereby reducing observer variability in histopathological interpretation.
病理学中的组织学诊断通常从与已知疾病实体相似的形态学模式的视觉识别开始。尽管数字病理学和增强智能已经在组织病理学中实现了反向图像搜索,但大多数现有框架依赖于单倍放大图像补丁和幻灯片级标签,限制了它们在不同粒度和尺度上捕获组织形态的能力。为了解决这个问题,我们提出了通过放大的渐进区域图像序列(PRISM),这是一个图像序列,可以在多个放大倍数中捕获上下文信息。在此基础上,我们引入了多上下文相似性评估(黏膜),这是一种基于prism的图像检索框架,它利用预训练的特征编码器而无需额外的微调。为了评估粘膜的性能,我们利用肺腺癌的组织学模式构建了参考和查询PRISM数据集。以三星医疗中心的全幻灯片图像(WSIs)作为参考和内部查询,以癌症基因组图谱(The Cancer Genome Atlas)作为外部查询。对于每个WSI,选择有代表性的感兴趣区域并转换为PRISM结构。两个棱镜之间的相似性是通过平均余弦相似度对应的补丁在相同的放大水平在所有放大计算。我们在不同的特征编码器、放大水平、接受域大小和内部/外部查询条件下进行了全面的评估。结果,粘膜与多倍放大优于单倍放大方法。例如,使用8倍放大UNI2-h编码器的粘膜的f1评分为0.8051 (95% CI: 0.7843-0.8267), mAP@5为0.7065 (95% CI: 0.6893-0.7250), mMV@5为0.8232 (95% CI: 0.8038-0.8434),均显著高于单倍放大基线(p <; 0.0001)。此外,混淆矩阵和目视检查证实,搜索结果与病理学家的形态学感知密切相关。综上所述,我们的研究表明,使用简单高效的黏膜多倍棱镜框架,无需微调,可以显著提高组织病理学中的图像搜索。我们预计粘膜可以帮助病理学家做出更准确和一致的诊断,从而减少组织病理学解释的观察者差异。
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引用次数: 0
Applications and challenges of utilizing digital pathology and AI-enabled workflows in clinical trials 在临床试验中利用数字病理学和人工智能工作流程的应用和挑战
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100542
Manu Sebastian , Harsh Batra , Monika Lamba Saini , Staci Kearney , Lorcan Sherry , Serge Alexanian , Michael Cohen , William Weber , Joe Lennerz , Anil V. Parwani
This is a comprehensive review on current utilization and challenges of digital pathology adoption in clinical trials and aims to provide a broad view on its impact on pathology review processes in clinical trials. It provides an overview of current pathology review practices in clinical trials and unique advantages digital pathology adoption can offer. The key areas including existing workflows, use case scenarios in different disease areas in clinical trials, including but not limited to patient identification and pre-screening, and regulatory aspects have been described with relevance. In addition, the review delves into the integration of genomics, AI, image analysis, radiology, and advanced computational pathology, to propose measures to enhance clinical trial outcomes. The current regulatory landscape around digital pathology adoption and potential future advancements in this field are also discussed as appropriate.
本文对数字病理学在临床试验中的应用现状和面临的挑战进行了全面的综述,旨在就其对临床试验病理审查过程的影响提供一个广泛的观点。它提供了当前病理审查实践的概述,在临床试验和独特的优势,数字化病理采用可以提供。关键领域包括现有工作流程、临床试验中不同疾病领域的用例情景,包括但不限于患者识别和预筛选,以及相关的监管方面。此外,本文还深入探讨了基因组学、人工智能、图像分析、放射学和先进计算病理学的整合,提出了提高临床试验结果的措施。此外,本文还讨论了当前围绕数字病理学采用的监管格局以及该领域未来的潜在进展。
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引用次数: 0
Iris RESTful Server and IrisTileSource: An Iris implementation for existing OpenSeaDragon viewers Iris RESTful Server和IrisTileSource:现有opensedragon查看器的Iris实现
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100530
Ryan Erik Landvater, Navin Kathawa, Mustafa Yousif, Ulysses Balis
The Iris File Extension (IFE) is a low overhead performance-oriented whole-slide image (WSI) file format designed to improve the image rendering experience for pathologists and simplify image management for system administrators. However, static hypertext transfer protocol (HTTP) file servers cannot natively stream subregions of high-resolution image files, such as the IFE. The majority of contemporary WSI viewer systems are designed as browser-based web applications and leverage OpenSeaDragon as the tile-based rendering framework. These systems convert WSI files to Deep Zoom Images (DZI) for compatibility with simple static HTTP file servers. To address this limitation, we have developed the Iris RESTful Server, a low-overhead HTTP server with a RESTful application programming interface (API) that is natively compatible with the DICOMweb WADO-RS API. Written in C++ with Boost Beast HTTP and Asio networking libraries atop the public IFE libraries, the server offers both security and high performance. Testing shows that a single Raspberry Pi equivalent system can handle a peak of 5061 req./s (average 3883 req./s) with a median latency of 21 ms on a private (i.e., hospital) network. We also developed and merged a new OpenSeaDragon TileSource, compatible with the Iris RESTful API, into the next OpenSeaDragon release, enabling simple and immediate drop-in replacement of DZI images within WSI viewer stacks. Designed as a secure cross-origin resource sharing microservice, this architecture includes detailed deployment instructions for new or existing WSI workflows, and the public examples.restful.irisdigitalpathology.org subdomain is provided as a development tool to accelerate WSI web viewer development. All relevant Iris software is available under the open-source MIT software license.
虹膜文件扩展(IFE)是一种低开销、以性能为导向的全幻灯片图像(WSI)文件格式,旨在改善病理学家的图像渲染体验,简化系统管理员的图像管理。但是,静态超文本传输协议(HTTP)文件服务器不能本地流式传输高分辨率图像文件的子区域,例如IFE。大多数当代WSI查看器系统被设计为基于浏览器的web应用程序,并利用opensedragon作为基于磁贴的渲染框架。这些系统将WSI文件转换为深度缩放图像(DZI),以便与简单的静态HTTP文件服务器兼容。为了解决这个限制,我们开发了Iris RESTful Server,这是一个低开销的HTTP服务器,具有RESTful应用程序编程接口(API),与DICOMweb WADO-RS API本地兼容。该服务器使用c++编写,在公共IFE库之上使用Boost Beast HTTP和Asio网络库,提供了安全性和高性能。测试表明,一个等效的树莓派系统可以处理5061 req的峰值。/s(平均3883 要求。/s),在私有(即医院)网络上的中位延迟为21 ms。我们还开发并合并了一个新的openseaddragon tile资源,与Iris RESTful API兼容,到下一个openseaddragon版本中,可以在WSI查看器堆栈中简单而直接地替换DZI图像。该架构被设计为安全的跨域资源共享微服务,包括新的或现有的WSI工作流的详细部署说明,并提供公共example.restful.irisdigitalpathology.org子域作为加速WSI web查看器开发的开发工具。所有相关的虹膜软件都是在开源的MIT软件许可下提供的。
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引用次数: 0
ADPv2: A hierarchical histological tissue type-annotated dataset for potential biomarker discovery of colorectal disease ADPv2:一个分层组织类型注释数据集,用于发现结直肠疾病的潜在生物标志物
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100537
Zhiyuan Yang , Kai Li , Sophia Ghamoshi Ramandi , Patricia Brassard , Abdelhakim Khellaf , Vincent Quoc-Huy Trinh , Jennifer Zhang , Lina Chen , Corwyn Rowsell , Sonal Varma , Kostas Plataniotis , Mahdi S. Hosseini
Computational pathology (CPath) leverages histopathology images to enhance diagnostic precision and reproducibility in clinical pathology. However, publicly available datasets for CPath that are annotated with extensive histological tissue type (HTT) taxonomies at a granular level remain scarce due to the significant expertise and high annotation costs required. Existing datasets, such as the Atlas of Digital Pathology (ADP), address this by offering diverse HTT annotations generalized to multiple organs, but limit the capability for in-depth studies on specific organ diseases. Building upon this foundation, we introduce ADPv2, a novel dataset focused on gastrointestinal histopathology. Our dataset comprises 20,004 image patches derived from healthy colon biopsy slides, annotated according to a hierarchical taxonomy of 32 distinct HTTs of 3 levels. Furthermore, we train a multilabel representation learning model following a two-stage training procedure on our ADPv2 dataset. By leveraging the VMamba model architecture, we achieve a mean average precision of 0.88 in multilabel colon HTT classification.. Finally, we show that our dataset is capable of an organ-specific in-depth study for potential biomarker discovery by analyzing the model's prediction behavior on tissues affected by different colon diseases, which reveals statistical patterns that confirm the two pathological pathways of colon cancer development. Our dataset is publicly available here: Part 1, Part 2, and Part 3.
计算病理学(CPath)利用组织病理学图像来提高临床病理学诊断的准确性和可重复性。然而,由于需要大量的专业知识和高昂的注释成本,在粒度级别上用广泛的组织学组织类型(HTT)分类法注释的CPath公开可用的数据集仍然很少。现有的数据集,如数字病理图谱(ADP),通过提供不同的HTT注释来解决这个问题,但限制了对特定器官疾病进行深入研究的能力。在此基础上,我们介绍了ADPv2,一个专注于胃肠道组织病理学的新数据集。我们的数据集包括来自健康结肠活检切片的200004个图像补丁,根据3个级别的32个不同的HTTs的分层分类法进行注释。此外,我们根据ADPv2数据集的两阶段训练过程训练了一个多标签表示学习模型。通过利用vamba模型架构,我们在多标签冒号HTT分类中实现了0.88的平均精度。最后,我们通过分析模型对受不同结肠疾病影响的组织的预测行为,表明我们的数据集能够对潜在的生物标志物发现进行器官特异性的深入研究,这揭示了确认结肠癌发展的两种病理途径的统计模式。我们的数据集可以在这里公开获取:第1部分、第2部分和第3部分。
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引用次数: 0
An integrated system from microscopy to AI for real-time object detection in endometrial cytology 从显微镜到人工智能的集成系统,用于子宫内膜细胞学中的实时目标检测
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100541
Mika Terasaki , Shun Tanaka , Ichito Shimokawa , Etsuko Toda , Shoichiro Takakuma , Yusuke Kajimoto , Shinobu Kunugi , Akira Shimizu , Yasuhiro Terasaki
Endometrial cytology, which is minimally invasive and available as an outpatient procedure, is widely used in Japan for early detection of endometrial cancer, but its diagnostic process is time-consuming and requires expert diagnosticians. We developed a real-time artificial intelligence (AI)-assisted system using a standard microscope, a charge-coupled device (CCD) camera, and the You-Only-Look-Once version 5x (YOLOv5x) (a well-established object detection model) to support endometrial cytology screening in resource-limited settings. A total of 146 pre-operative cytology cases were collected, and the model was trained to detect abnormal cell clusters. The system was evaluated in real-time using a CCD camera, and its diagnostic performance was compared with that of three pathologists and four medical students. In an independent test of 20 cases, the AI model achieved an accuracy of 85%, showing promising performance comparable to the average accuracy of 75% among human evaluators. Furthermore, the median diagnostic time was reduced by approximately 45% with AI assistance. The impact of AI support varied by user expertise, with notable improvements among non-specialists. This proof-of-concept study demonstrates the feasibility and potential of affordable, real-time AI support for endometrial cytology using widely available equipment. Further validation with larger, multicenter datasets is warranted to confirm the generalizability and clinical utility of this approach.
子宫内膜细胞学检查是一种微创的门诊手术,在日本广泛用于子宫内膜癌的早期检测,但其诊断过程耗时且需要专家诊断。我们开发了一种实时人工智能(AI)辅助系统,使用标准显微镜,电荷耦耦器(CCD)相机和You-Only-Look-Once version 5x (YOLOv5x)(一种完善的对象检测模型)来支持资源有限环境下的子宫内膜细胞学筛查。收集术前细胞学检查病例146例,训练模型检测异常细胞簇。利用CCD摄像机对该系统进行实时评价,并与3名病理学家和4名医学生的诊断效果进行比较。在20个案例的独立测试中,人工智能模型达到了85%的准确率,与人类评估者75%的平均准确率相当。此外,在人工智能的帮助下,中位诊断时间减少了约45%。人工智能支持的影响因用户的专业知识而异,在非专业人士中有显著改善。这项概念验证研究表明,使用广泛可用的设备,可负担得起的实时人工智能支持子宫内膜细胞学的可行性和潜力。在更大的、多中心的数据集上进一步验证是有必要的,以确认该方法的普遍性和临床实用性。
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引用次数: 0
A machine learning model of lamina propria fibrosis in eosinophilic esophagitis for prediction of fibrostenotic disease 嗜酸性粒细胞性食管炎固有层纤维化的机器学习模型预测纤维狭窄性疾病
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100538
Priyadharshini Sivasubramaniam , Abdelrahman Shabaan , Rofyda Elhalaby , Bashar Hasan , Ameya A. Patil , Saadiya Nazli , Adilson DaCosta , Byoung Uk Park , Lindsey Smith , Taofic Mounajjed , Stephen M. Lagana , Chamil Codipilly , Puanani Hopson , Imad Absah , Christopher P. Hartley , Rondell P. Graham , Roger K. Moreira

Background

Eosinophilic esophagitis (EoE) is a chronic immune-mediated disease that can progress to fibrostenotic complications. Lamina propria fibrosis (LPF) plays a critical role in this progression but is difficult to assess reliably in routine biopsies. We aimed to develop and validate an artificial intelligence (AI) model to quantify LPF on hematoxylin and eosin (H&E)-stained slides and to evaluate its ability to predict fibrostenotic disease.

Methods

We used a cloud-based platform (Aiforia Inc., Cambridge, MA, USA) to train a supervised AI model to recognize several histological features of EoE, including LPF. Our validation cohort consisted of 213 esophageal biopsy whole-slide images, including 100 adult and 113 pediatric samples with mucosal eosinophilia, which were prospectively evaluated in our anatomic pathology service between 2020 and 2021 using a standardized histological scoring system. AI-based LPF scores were correlated with the development of fibrostenotic disease on subsequent endoscopies after a median follow-up time of 31.4 months.

Results

The AI fibrosis score correlated with pathologist-determined LPF (Spearman's Rs = 0.64–0.69, p < 0.0001) and outperformed pathologists' assessments in predicting fibrostenotic outcomes. Higher AI fibrosis scores were associated with the development of rings, strictures, and need for dilatation on follow-up (p < 0.01), including in cases deemed histologically inadequate by pathologists and in the subgroup without prior strictures. In a Cox Proportional-Hazards model, the AI fibrosis score was an independent predictor of strictures (C-index = 0.73, p = 0.004). Importantly, meaningful predictions were achievable with smaller amounts of lamina propria than traditionally deemed sufficient.

Conclusion

This study demonstrates that AI-based quantification of LPF on routine H&E slides provides an objective and clinically meaningful assessment of fibrosis in EoE. The AI fibrosis score predicts fibrostenotic disease more consistently than conventional pathology evaluation and may improve risk stratification even in limited biopsy samples. Integration of digital pathology tools may enhance histological assessment of fibrosis in EoE and support clinical decision-making.
嗜酸性粒细胞性食管炎(EoE)是一种慢性免疫介导的疾病,可发展为纤维狭窄并发症。固有层纤维化(LPF)在这种进展中起关键作用,但在常规活检中难以可靠地评估。我们旨在开发和验证人工智能(AI)模型,以量化苏木精和伊红(H&;E)染色玻片上的LPF,并评估其预测纤维狭窄性疾病的能力。方法我们使用基于云的平台(Aiforia Inc., Cambridge, MA, USA)来训练一个有监督的AI模型来识别EoE的几种组织学特征,包括LPF。我们的验证队列包括213张食管活检全切片图像,包括100例成人和113例儿童粘膜嗜酸性粒细胞增生样本,这些样本在2020年至2021年期间在我们的解剖病理学服务中使用标准化组织学评分系统进行前瞻性评估。在中位随访31.4 个月后,基于人工智能的LPF评分与随后的内窥镜检查中纤维狭窄性疾病的发展相关。结果AI纤维化评分与病理学确定的LPF相关(Spearman’s Rs = 0.64-0.69,p <; 0.0001),在预测纤维狭窄结局方面优于病理学评估。较高的AI纤维化评分与环、狭窄的发展和随访时需要扩张相关(p <; 0.01),包括病理学家认为组织学不充分的病例和先前没有狭窄的亚组。在Cox比例风险模型中,AI纤维化评分是狭窄的独立预测因子(c指数 = 0.73,p = 0.004)。重要的是,有意义的预测是可以实现较少的固有层比传统认为足够的。结论本研究表明,基于人工智能的常规H&;E载玻片LPF定量为评估EoE纤维化提供了客观且具有临床意义的方法。AI纤维化评分预测纤维狭窄性疾病比常规病理评估更一致,即使在有限的活检样本中也可能改善风险分层。数字病理工具的整合可以增强EoE纤维化的组织学评估并支持临床决策。
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引用次数: 0
PANDA-PLUS: Improved dataset of prostate whole slide images from PANDA Challenge with pixel-level expert annotations PANDA- plus:改进的来自PANDA Challenge的前列腺整张幻灯片图像数据集,具有像素级专家注释
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100540
Spencer Hopson, Carson Mildon, Corbyn Kubalek, Joshua Ebbert, Ryan Vance, Lauren Laverty, Paul Urie, Dennis Della Corte
Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image dataset derived from PANDA images with improved pixel-level annotations, as well as an accompanying annotation pipeline that reduces pathologists' time commitment. We present a detailed comparative analysis between PANDA-PLUS and PANDA using Gleason score and ISUP grade, supported by agreement values, κ, and PABAK under multiple weighting schemes. The results demonstrate consistently lower grading in PANDA-PLUS, with disagreement patterns especially pronounced at higher grades. We also demonstrate through single rater grading of various annotation granularities how slide- and patch-level labels may distort grading proportions and alter image scores. PANDA-PLUS not only improves annotation granularity and reduces label noise but also exposes potential grading errors in the original PANDA dataset. We present PANDA-PLUS's annotations as an improved alternative to the PANDA labels and conclude that it represents a step forward in the development of higher-quality public datasets for clinical AI applications in prostate cancer pathology.
基于人工智能(AI)的全幻灯片图像前列腺癌检测在解决全球病理学家短缺问题的同时提高了临床一致性。数字幻灯片和改进的图像分析方法鼓励创建工具来帮助WSI分类。尽管有了很大的进步,但这些工具仍然受到现有训练数据的限制。目前可公开获得的数据集,如Kaggle的PANDA挑战,虽然规模很大,但依赖于可能引入噪声和限制模型可靠性的滑动级标签。其他一些包含详细的注释,但由于手工处理工作,其大小较小。在这项工作中,我们介绍了PANDA- plus,这是一个来自PANDA图像的546张图像数据集,具有改进的像素级注释,以及附带的注释管道,可以减少病理学家的时间投入。我们使用Gleason评分和ISUP评分,并在多重加权方案下使用协议值、κ和PABAK支持,对PANDA- plus和PANDA进行了详细的比较分析。结果显示,PANDA-PLUS的评分始终较低,在较高的评分中,差异模式尤为明显。我们还通过单个分级器对各种标注粒度进行分级,演示了幻灯片级和补丁级标签如何扭曲分级比例并改变图像分数。PANDA- plus不仅提高了标注粒度,减少了标注噪声,而且暴露了原始PANDA数据集中潜在的分级错误。我们提出PANDA- plus的注释作为PANDA标签的改进替代品,并得出结论,它代表了在开发更高质量的公共数据集方面向前迈进了一步,用于临床人工智能在前列腺癌病理学中的应用。
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引用次数: 0
Biological feature-based machine learning in histopathological images: a systematic review 组织病理学图像中基于生物特征的机器学习:系统综述
Q2 Medicine Pub Date : 2026-01-01 DOI: 10.1016/j.jpi.2025.100539
Stéphane Treillard , Robin Schwob , Sandrine Mouysset , Pierre Brousset , Sylvain Cussat-Blanc , Camille Franchet
Digital pathology has recently led to significant advancements in the field of microscopic image analysis, particularly regarding the increasing use of Deep Learning methods. These models represent the state-of-the-art in histopathological slide analysis, but Deep Learning features remain difficult to interpret, despite recent developments in post hoc explainability frameworks. In contrast, features extracted from biological objects—such as nuclei, cells or tissues—are supposed to be more grounded in pathologists' a priori knowledge. Accordingly, Machine Learning based on handcrafted features represents another paradigm of explainability and may stand as a complementary method to Deep Learning to assist pathologists.
In order to perceive how biological features have been used in hematoxylin & eosin microscopic images to address medical questions, we conducted a systematic review of articles published from January 2005 to May 2025, adhering to PRISMA guidelines.
A total of 97 articles were analyzed from the PubMed, IEEE, and ACM databases. Three primary categories of features—texture/color, morphology and topology—were both identified and thoroughly described. These features were most frequently derived from segmented cells and tissues in 80 and 28 studies, respectively. They were used to address seven types of medical questions: “normal vs diseased”, disease subtyping, tumor grading, phenotyping, object detection, prognosis and treatment-response prediction.
We discussed methodological and reporting limitations of these studies, highlighting the difficulty to assess the potential impact of such methods. Among the most common concerns, we found features difficult to interpret, data leakage, and inadequate sample sizes. Nevertheless, we also focused on promising domain-inspired feature engineering that provides better explainability and specificity. This kind of features associated with more methodological rigor may increase the relevance and reliability of AI models, and also raise new research avenues in pathology.
数字病理学最近在显微图像分析领域取得了重大进展,特别是关于越来越多地使用深度学习方法。这些模型代表了组织病理学切片分析的最新技术,但深度学习的特征仍然难以解释,尽管最近在事后解释框架方面取得了进展。相比之下,从生物物体中提取的特征——如细胞核、细胞或组织——被认为是基于病理学家的先验知识。因此,基于手工特征的机器学习代表了另一种可解释性范式,可以作为深度学习的补充方法来帮助病理学家。为了了解如何利用苏木精伊红显微图像中的生物学特征来解决医学问题,我们根据PRISMA指南对2005年1月至2025年5月发表的文章进行了系统回顾。共分析了来自PubMed、IEEE和ACM数据库的97篇文章。三个主要类别的特征-纹理/颜色,形态和拓扑-都被识别和彻底描述。在80项和28项研究中,这些特征最常来自分节的细胞和组织。他们被用来解决七种类型的医学问题:“正常与患病”、疾病亚型、肿瘤分级、表型、目标检测、预后和治疗反应预测。我们讨论了这些研究的方法和报告局限性,强调了评估这些方法的潜在影响的困难。在最常见的问题中,我们发现了难以解释的特性、数据泄漏和样本量不足。尽管如此,我们也专注于有前途的领域启发特征工程,它提供了更好的可解释性和特异性。这种与更严谨的方法相关的特征可能会增加人工智能模型的相关性和可靠性,并为病理学提供新的研究途径。
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引用次数: 0
Leveraging sequence-to-sequence models for semantic annotation of Dutch pathology reports 利用序列到序列模型对荷兰病理学报告进行语义注释
Q2 Medicine Pub Date : 2025-12-05 DOI: 10.1016/j.jpi.2025.100534
M. Siepel , G.T.N. Burger , Q.J.M. Voorham , R. Cornet , I. Calixto , I. Vagliano
Palga Foundation is responsible for indexing Dutch pathology data across the Netherlands, which relies on annotations of pathology reports. These annotations, derived from the conclusion text, consist of codes from the Palga thesaurus, serving patient care and scientific research. However, manual annotation by pathologists is both labor-intensive and prone to errors. Therefore, in this study, we seek to leverage sequence-to-sequence transformer models, particularly Text-To-Text Transfer Transformer (T5)-based models, to generate these annotations. Additionally, we investigate a constrained decoding (CD) approach that encodes domain knowledge. We compare a standard multilingual T5 model (mT5) with our own T5 model (PaTh5.NL) pre-trained using Palga data with the goal of better aligning the model's learned representations with the specific structure, terminology, and annotation conventions used in Dutch pathology reports. We fine-tune both pre-trained models using default (DD) and CD and compare both decoding strategies. Performance is assessed using Bilingual Evaluation Understudy (BLEU) scores for quantitative evaluation and case-based evaluations for qualitative assessment, where we use the generated codes to retrieve patients from the Palga database. Quantitative evaluations indicated that our two fine-tuned PaTh5.NL models significantly outperformed the fine-tuned mT5 model, particularly for shorter histology and cytology reports, but performance of all models declined on longer or complex reports. The case-based evaluation revealed that, despite higher BLEU scores, the PaTh5.NL models did not consistently outperform the mT5 model in retrieving relevant patients. This study demonstrates that fine-tuned T5-based models can enhance the annotation process for Dutch pathology reports, though challenges remain regarding complex conclusion texts, especially in histology and autopsy reports. Future research should focus on expanding gold-standard datasets and developing post-processing algorithms to improve annotations' generalization.
帕尔加基金会负责索引荷兰病理数据在整个荷兰,这依赖于病理报告的注释。这些注解,源自结论文本,由来自帕尔加同义词典的代码组成,服务于病人护理和科学研究。然而,病理学家的手工注释既费力又容易出错。因此,在本研究中,我们寻求利用序列到序列转换器模型,特别是基于文本到文本传输转换器(T5)的模型,来生成这些注释。此外,我们研究了一种对领域知识进行编码的约束解码(CD)方法。我们将标准的多语种T5模型(mT5)与我们自己的T5模型(PaTh5.NL)进行比较,该模型使用Palga数据进行预训练,目的是更好地将模型的学习表征与荷兰语病理报告中使用的特定结构、术语和注释惯例相一致。我们使用默认(DD)和CD对预训练模型进行微调,并比较两种解码策略。使用双语评估替代研究(BLEU)分数进行定量评估,使用基于病例的评估进行定性评估,其中我们使用生成的代码从Palga数据库检索患者。定量评估表明,我们的两个微调PaTh5。NL模型的表现明显优于经过微调的mT5模型,特别是对于较短的组织学和细胞学报告,但所有模型的表现在较长或复杂的报告中都有所下降。基于病例的评估显示,尽管BLEU得分较高,但PaTh5。在检索相关患者时,NL模型的表现并不总是优于mT5模型。本研究表明,微调的基于t5的模型可以增强荷兰病理学报告的注释过程,尽管在复杂的结论文本方面仍然存在挑战,特别是在组织学和尸检报告中。未来的研究应该集中在扩展金标准数据集和开发后处理算法以提高注释的泛化。
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引用次数: 0
Developing a smart and scalable tool for histopathological education—PATe 2.0 开发一个智能和可扩展的组织病理学教育工具- pate 2.0
Q2 Medicine Pub Date : 2025-12-05 DOI: 10.1016/j.jpi.2025.100535
Lina Winter , Annalena Artinger , Hendrik Böck , Vignesh Ramakrishnan , Bruno Reible , Jan Albin , Peter J. Schüffler , Georgios Raptis , Christoph Brochhausen
Digital microscopy plays a crucial role in pathology education, providing scalable and standardized access to learning resources. In response, we present PATe 2.0, a scalable redeveloped web-application of the former PATe system from 2015. PATe 2.0 was developed using an agile, iterative process and built on a microservices architecture to ensure modularity, scalability, and reliability. It integrates a modern web-based user interface optimized for desktop and tablet use and automates key workflows such as whole-slide image uploads and processing. Performance tests demonstrated that PATe 2.0 significantly reduces tile request times compared to PATe, despite handling larger tiles. The platform supports open formats like DICOM and OpenSlide, enhancing its interoperability and adaptability across institutions. PATe 2.0 represents a robust digital microscopy solution in pathology education enhancing usability, performance, and flexibility. Its design enables future integration of research algorithms and highlights it as a pivotal tool for advancing pathology education and research.
数字显微镜在病理学教育中起着至关重要的作用,提供了可扩展和标准化的学习资源。作为回应,我们提出了PATe 2.0,这是2015年以前的PATe系统的可扩展的重新开发的web应用程序。PATe 2.0是使用敏捷的迭代过程开发的,并构建在微服务体系结构上,以确保模块化、可伸缩性和可靠性。它集成了一个现代的基于web的用户界面,为桌面和平板电脑的使用进行了优化,并自动化了关键的工作流程,如整张幻灯片图像的上传和处理。性能测试表明,尽管处理的贴图更大,但与PATe相比,PATe 2.0显著减少了贴图请求时间。该平台支持DICOM和OpenSlide等开放格式,增强了其跨机构的互操作性和适应性。PATe 2.0代表了病理学教育中强大的数字显微镜解决方案,增强了可用性,性能和灵活性。它的设计使未来的研究算法的整合,并突出了它作为一个关键的工具,推进病理教育和研究。
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引用次数: 0
期刊
Journal of Pathology Informatics
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