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bioRxiv · 10.64898/2025.12.18.695211

Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E

Mandal, S.·de Almeida, J. G.·Papanikolaou, N.·Graham, T. A.
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Abstract

Cell phenotyping in histopathology samples is essential for diagnostic and research workflows. However, human expert annotation requires significant time and expertise while being affected by inter-observer variability. Here, we present Classpose, an easily trainable framework for cell segmenting and phenotyping built on top of Cellpose-SAM with state-of-the-art performance across 6 distinct datasets, outperforming competing methods. We show that this requires fine-tuning the entire network, highlighting how instance segmentation is a poor objective for downstream cellular classification. We apply it to a large whole slide image (WSI) colorectal cancer (CRC) cohort (SurGen) and show that Classpose-derived cellular organisation and morphology features can be used to determine novel spatial morphological phenotypes for clinically relevant molecular conditions (MMR deficiency, BRAF mutations, KRAS mutations) and to predict these same molecular conditions. We make Classpose models available and provide a user-friendly QuPath extension for widespread use by the digital pathology community.

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Mandal, S., de Almeida, J. G., Papanikolaou, N., Graham, T. A.. 2025-12-22. Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E. https://doi.org/10.64898/2025.12.18.695211

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