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bioRxiv · 10.64898/2026.11.05.764509

Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics

Jeong, Y.·Lee, H.·Lee, D.·Kim, H.-M.·Kim, S.-H.·Park, S.·Bae, J.·Cho, E. S.·Choi, Y.-L.·Kwon, O.·Kim, J.-I.·Park, J.
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Abstract

Cell-type identification in spatial transcriptomics often relies on cell segmentation, which can introduce inaccuracies in cell boundaries and transcript assignment. Segmentation-free or cell-free methods have been developed to completely avoid cell segmentation, but inaccurate cell typing hinder accurate downstream analysis. Here, we introduce SSAF-T, a segmentation-free agentic framework that identifies cell types directly from spatial gene expression without predefined reference datasets. For the reference-free cell typing, SSAF-T incorporates CeLLMan, which employs expert-level agents for each organ to annotate cell types using a literature-grounded knowledge graph. We benchmark SSAF-T on both array-based and imaging-based spatial transcriptomics datasets in terms of accuracy, reproducibility, and scalability. We further show that SSAF-T provides an accurate cell segmentation based on the segmentation-free mapping, which ensure compatibility to existing downstream analysis ecosystem, and eventually enable quantitative analysis at single-cell level.

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Jeong, Y., Lee, H., Lee, D., Kim, H.-M., Kim, S.-H., Park, S., Bae, J., Cho, E. S., Choi, Y.-L., Kwon, O., Kim, J.-I., Park, J.. 2026-11-06. Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics. https://doi.org/10.64898/2026.11.05.764509

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