A Foundation Model for Cell Segmentation

Israel, U.; Marks, M.; Dilip, R.; Li, Q.; Schwartz, M. S.; Pradhan, E.; Pao, E.; Li, S.; Pearson-Goulart, A.; Perona, P.; Gkioxari, G.; Barnowski, R.; Yue, Y.; Van Valen, D. A.

doi:10.1101/2023.11.17.567630

bioRxiv · 10.1101/2023.11.17.567630

A Foundation Model for Cell Segmentation

Israel, U.·Marks, M.·Dilip, R.·Li, Q.·Schwartz, M. S.·Pradhan, E.·Pao, E.·Li, S.·Pearson-Goulart, A.·Perona, P.·Gkioxari, G.·Barnowski, R.·Yue, Y.·Van Valen, D. A.

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Abstract

Cells are a fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, most models are specialist models that work well for specific domains but cannot be applied across domains or scale well with large amounts of data. In this work, we present CellSAM, a universal model for cell segmentation that generalizes across diverse cellular imaging data. CellSAM builds on top of the Segment Anything Model (SAM) by developing a prompt engineering approach for mask generation. We train an object detector, CellFinder, to automatically detect cells and prompt SAM to generate segmentations. We show that this approach allows a single model to achieve human-level performance for segmenting images of mammalian cells, yeast, and bacteria collected across various imaging modalities. We show that CellSAM has strong zero-shot performance and can be improved with a few examples via few-shot learning. Additionally, we demonstrate how CellSAM can be applied across diverse bioimage analysis workflows. A deployed version of CellSAM is available at https://cellsam.deepcell.org/.

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Israel, U., Marks, M., Dilip, R., Li, Q., Schwartz, M. S., Pradhan, E., Pao, E., Li, S., Pearson-Goulart, A., Perona, P., Gkioxari, G., Barnowski, R., Yue, Y., Van Valen, D. A.. 2023-11-20. A Foundation Model for Cell Segmentation. https://doi.org/10.1101/2023.11.17.567630

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