StainNet让病理模型学会分析免疫组化和特殊染色图像,提升临床实用价值。
StainNet: Scaling Self-Supervised Foundation Models on Immunohistochemistry and Special Stains for Computational Pathology
- 用自蒸馏自监督学习训练,专为免疫组化和特殊染色图像设计
- 在超140万张切片图上预训练,覆盖2万余张全幻灯片
- 适合做非H&E染色图像的特征提取,尤其对小样本任务表现优
基于自监督学习(SSL)的大规模组织学图像预训练基础模型显著推动了计算病理学发展。这些模型可作为区域感兴趣区(ROI)图像分析或全幻灯片图像(WSI)中基于多实例学习(MIL)的切片级特征提取器。现有病理基础模型(PFMs)通常仅在苏木精-伊红(H&E)染色图像上预训练,但在临床中广泛使用的免疫组化(IHC)和特殊染色图像上表现受限。为此,我们提出StainNet,一组基于视觉变压器(ViT)架构、专为病理IHC和特殊染色图像设计的自监督基础模型。StainNet包含一个ViT-Small和一个ViT-Base模型,均在超过140万张从20,231个公开IHC与特殊染色全幻灯片中提取的图像块上,通过自蒸馏SSL方法训练。我们通过三个院内切片级IHC分类任务、三个院内ROI级特殊染色任务及两个公开的ROI级IHC分类任务评估其性能,结果表明其具备强大能力。还进行了少样本学习和检索评估,并与近期更大规模的PFMs对比,进一步凸显其优势。模型权重已开源:https://github.com/WonderLandxD/StainNet。
原文摘要 · Abstract (English)
Foundation models trained with self-supervised learning (SSL) on large-scale histological images have significantly accelerated the development of computational pathology. These models can serve as backbones for region-of-interest (ROI) image analysis or patch-level feature extractors in whole-slide images (WSIs) based on multiple instance learning (MIL). Existing pathology foundation models (PFMs) are typically pre-trained on Hematoxylin-Eosin (H\&E) stained pathology images. However, images such as immunohistochemistry (IHC) and special stains are also frequently used in clinical practice. PFMs pre-trained mainly on H\&E-stained images may be limited in clinical applications involving these non-H\&E images. To address this issue, we propose StainNet, a collection of self-supervised foundation models specifically trained for IHC and special stains in pathology images based on the vision transformer (ViT) architecture. StainNet contains a ViT-Small and a ViT-Base model, both of which are trained using a self-distillation SSL approach on over 1.4 million patch images extracted from 20,231 publicly available IHC and special staining WSIs in the HISTAI database. To evaluate StainNet models, we conduct experiments on three in-house slide-level IHC classification tasks, three in-house ROI-level special stain and two public ROI-level IHC classification tasks to demonstrate their strong ability. We also perform ablation studies such as few-ratio learning and retrieval evaluations, and compare StainNet models with recent larger PFMs to further highlight their strengths. The StainNet model weights are available at https://github.com/WonderLandxD/StainNet.
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