CytoFormer: A Molecularly Supervised Cell Foundation Model for Histopathology Cell Classification
Identifying cell types directly from routine haematoxylin and eosin (H&E) histology would enable single-cell analysis at scale, but training such models has relied on manual pathologist annotations, which are slow, expensive and unreliable for many cell types. We instead supervise morphology with molecules. Imaging-based spatial transcriptomics profiles individual cells in situ on a section that can afterwards be stained with H&E, so that molecular identity and morphology are observed for the same physical cell. We assembled 81 such paired Xenium sections spanning 16 organs, derived per-cell labels by clustering, marker-gene annotation, organ-wise human review and quality control, and map...
| Authors | Jialu Yao, Songhao Li, Alina Yu et al. |
|---|---|
| Primary category | cs.CV |
| Published | 17 August 2026 |
| Last updated at source | 17 August 2026 |
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