In digital pathology, the traditional method for deep learning-based image segmentation typically involves a two-stage process: initially segmenting high-resolution whole slide images (WSI) into smaller patches (e.g., 256x256, 512x512, 1024x1024) and subsequently reconstructing them to their original scale. This method often struggles to capture the complex details and vast scope of WSIs. In this paper, we propose the holistic histopathology (HoloHisto) segmentation method to achieve end-to-end segmentation on gigapixel WSIs, whose maximum resolution is above 80,000$\times$70,000 pixels. HoloHisto fundamentally shifts the paradigm of WSI segmentation to an end-to-end learning fashion with 1) a large (4K) resolution base patch for elevated visual information inclusion and efficient processing, and 2) a novel sequential tokenization mechanism to properly model the contextual relationships and efficiently model the rich information from the 4K input. To our best knowledge, HoloHisto presents the first holistic approach for gigapixel resolution WSI segmentation, supporting direct I/O of complete WSI and their corresponding gigapixel masks. Under the HoloHisto platform, we unveil a random 4K sampler that transcends ultra-high resolution, delivering 31 and 10 times more pixels than standard 2D and 3D patches, respectively, for advancing computational capabilities. To facilitate efficient 4K resolution dense prediction, we leverage sequential tokenization, utilizing a pre-trained image tokenizer to group image features into a discrete token grid. To assess the performance, our team curated a new kidney pathology image segmentation (KPIs) dataset with WSI-level glomeruli segmentation from whole mouse kidneys. From the results, HoloHisto-4K delivers remarkable performance gains over previous state-of-the-art models.
Norwegian University of Science and Technology（挪威科技大学）；St. Olavs Hospital, Trondheim University Hospital（圣奥拉夫医院，特隆赫姆大学医院）；SINTEF Digital（挪威科技工业研究院数字研究所）
The University of Tokyo（东京大学）；RIKEN（理化学研究所）；The Japanese Society of Pathology（日本病理学会）；Kyoto University（京都大学）；Tokyo Medical and Dental University（东京医科齿科大学）；National Institute of Informatics（国立信息学研究所）
SAGE: Shape-Adapting Gated Experts for Adaptive Histopathology Image Segmentation
University of Science, VNU-HCM（越南国家大学科学学院）；Trivita AI；University of Technology, VNU-HCM（越南国家大学技术学院）；Michigan State University, USA（美国密歇根州立大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Exploring shared memory architectures for end-to-end gigapixel deep learning
Vanderbilt University（范德堡大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；National Institutes of Health（美国国立卫生研究院）；Vanderbilt University Medical Center（范德堡大学医学中心）；Veterans Affairs Tennessee Valley Healthcare System（退伍军人事务部田纳西谷医疗系统）
LSP-DETR: Efficient and Scalable Nuclei Segmentation in Whole-Slide Images
Masaryk University, Faculty of Informatics（马萨里克大学信息学院）；Masaryk University, Institute for Computer Science（马萨里克大学计算机科学研究所）；Masaryk Memorial Cancer Institute（马萨里克纪念癌症研究所）
University of Warwick（华威大学）；University of Birmingham（伯明翰大学）；The Alan Turing Institute（艾伦·图灵研究所）；University Hospitals Coventry & Warwickshire（考文垂与沃里克郡大学医院）
Magnification-Aware Distillation (MAD): A Self-Supervised Framework for Unified Representation Learning in Gigapixel Whole-Slide Images
Center for Applied Artificial Intelligence, University of Kentucky（应用人工智能中心，肯塔基大学）；Sanders-Brown Center on Aging, University of Kentucky（老龄化桑德斯-布朗中心，肯塔基大学）；Department of Electrical and Computer Engineering, University of Kentucky（电气与计算机工程系，肯塔基大学）；Division of Neuropathology, University of Pittsburgh（神经病理学部，匹兹堡大学）；Department of Biomedical Informatics, Emory University（生物医学信息学系，埃默里大学）；Department of Pathology and Laboratory Medicine, University of California Davis（病理学与实验室医学系，加州大学戴维斯分校）；Department of Laboratory Medicine and Pathology, University of Texas Health（实验室医学与病理学系，德克萨斯大学健康科学中心）
A Survey on Cell Nuclei Instance Segmentation and Classification: Leveraging Context and Attention
INESC TEC - Institute for Systems and Computer Engineering, Technology and Science（INESC TEC系统与计算机工程、技术与科学研究所）；University of Porto - Faculty of Engineering（波尔图大学工程学院）；IMP Diagnostics（IMP诊断公司）；Portuguese Oncology Institute of Porto (IPO Porto)（波尔图葡萄牙肿瘤研究所）；University of Porto (ICBAS-UP)（波尔图大学（ICBAS-UP））；FCTUC - Faculty of Science and Technology, University of Coimbra（科英布拉大学科学与技术学院（FCTUC））
PySlyde: A Lightweight, Open-Source Toolkit for Pathology Preprocessing
PharosAI；King’s College London（国王学院伦敦分校）；School of Cancer and Pharmaceutical Sciences（癌症与制药科学学院）；The Alan Turing Institute（艾伦·图灵研究所）；The Francis Crick Institute（弗朗西斯·克里克研究所）；Barts Life Sciences（巴特斯生命科学）；Barts Health NHS Trust（巴特斯健康 NHS信托）；eResearch
Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；Broad Institute of Harvard and MIT（哈佛-麻省理工学院博德研究所）；Dana-Farber Cancer Institute（达纳-法伯癌症研究所）
