PathoSAM让病理图像中的细胞分割更智能,无需重新训练就能适应新数据。
Segment Anything for Histopathology
- 基于多样化数据微调SAM,构建专用病理细胞分割模型
- 在自动与交互式分割任务中达到当前最优性能
- 支持多种分割场景,代码开源且兼容主流标注工具
细胞分割是数字病理分析中的关键任务。现有自动化方法在面对分布不同的新数据时表现不佳,常需人工标注并重新训练模型。视觉基础模型(如SAM)为自动与交互式分割提供了更鲁棒的方案。尽管在自然图像上取得成功,但针对病理图像的细胞分割基础模型仍为空白。现有适配尝试虽有一定成效,但未形成完整解决方案。为此,我们提出PathoSAM,一个基于多样本训练的视觉基础模型,专用于病理图像中的细胞分割。大量实验表明,其在自动与交互式细胞实例分割任务中达到新基准。此外,该模型还可扩展至语义细胞分割任务,性能优于多数主流方法,略逊于最先进模型CellViT。模型与代码已开源,支持全切片图像分割,并兼容主流标注工具。项目地址:https://github.com/computational-cell-analytics/patho-sam。
原文摘要 · Abstract (English)
Nucleus segmentation is an important analysis task in digital pathology. However, methods for automatic segmentation often struggle with new data from a different distribution, requiring users to manually annotate nuclei and retrain data-specific models. Vision foundation models (VFMs), such as the Segment Anything Model (SAM), offer a more robust alternative for automatic and interactive segmentation. Despite their success in natural images, a foundation model for nucleus segmentation in histopathology is still missing. Initial efforts to adapt SAM have shown some success, but did not yet introduce a comprehensive model for diverse segmentation tasks. To close this gap, we introduce PathoSAM, a VFM for nucleus segmentation, based on training SAM on a diverse dataset. Our extensive experiments show that it is the new state-of-the-art model for automatic and interactive nucleus instance segmentation in histopathology. We also demonstrate how it can be adapted for other segmentation tasks, including semantic nucleus segmentation. For this task, we show that it yields results better than popular methods, while not yet beating the state-of-the-art, CellViT. Our models are open-source and compatible with popular tools for data annotation. We also provide scripts for whole-slide image segmentation. Our code and models are publicly available at https://github.com/computational-cell-analytics/patho-sam.
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