用病理大模型+空间转录组,从病理切片预测细胞组成。
Integrating Pathology Foundation Models and Spatial Transcriptomics for Cellular Decomposition from Histology Images
- 用预训练病理大模型提取特征,轻量MLP回归预测细胞比例。
- 在不进行昂贵的空间转录组实验下,准确还原细胞组成。
- 适合想低成本获取细胞图谱的研究者使用。
数字病理与深度学习的快速发展催生了病理基础模型,有望在无需微调的情况下统一解决多种疾病下的病理问题。与此同时,空间转录组技术实现了对苏木精-伊红(H&E)染色病理切片的基因表达定位,使我们能以细胞级粒度解析现有病理图像。本文提出一种轻量、高效训练的方法,通过利用预训练病理基础模型提取的信息丰富特征嵌入,直接从H&E染色图像预测细胞组成。方法在cell2location推导的细胞类型丰度上训练轻量多层感知机(MLP)回归器,有效从基础模型中蒸馏知识,实现无需实际进行空间转录组即可精准预测细胞类型组成。相比现有方法如Hist2Cell,本方法性能相当但计算复杂度显著降低。
原文摘要 · Abstract (English)
The rapid development of digital pathology and modern deep learning has facilitated the emergence of pathology foundation models that are expected to solve general pathology problems under various disease conditions in one unified model, with or without fine-tuning. In parallel, spatial transcriptomics has emerged as a transformative technology that enables the profiling of gene expression on hematoxylin and eosin (H&E) stained histology images. Spatial transcriptomics unlocks the unprecedented opportunity to dive into existing histology images at a more granular, cellular level. In this work, we propose a lightweight and training-efficient approach to predict cellular composition directly from H&E-stained histology images by leveraging information-enriched feature embeddings extracted from pre-trained pathology foundation models. By training a lightweight multi-layer perceptron (MLP) regressor on cell-type abundances derived via cell2location, our method efficiently distills knowledge from pathology foundation models and demonstrates the ability to accurately predict cell-type compositions from histology images, without physically performing the costly spatial transcriptomics. Our method demonstrates competitive performance compared to existing methods such as Hist2Cell, while significantly reducing computational complexity.
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