CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images

Wei, Z.; Curtin, I.; Kyere, F. A.; Borland, D.; Yi, H.; Kim, M.; Dere, M.; McCormick, C. M.; Krupa, O.; Shih, Y.-Y. I.; Zylka, M. J.; Stein, J. L.; Wu, G.

doi:10.64898/2026.03.17.712391

bioRxiv · 10.64898/2026.03.17.712391

CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images

Wei, Z.·Curtin, I.·Kyere, F. A.·Borland, D.·Yi, H.·Kim, M.·Dere, M.·McCormick, C. M.·Krupa, O.·Shih, Y.-Y. I.·Zylka, M. J.·Stein, J. L.·Wu, G.

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Abstract

Advances in tissue clearing and light-sheet microscopy enable cellular resolution whole-brain 3D imaging. However, whole-brain quantification tools do not yet meet demands for efficiency or assess morphometry. Here we present CellPheno, a 3D nuclei instance segmentation framework for high-throughput cellular phenotyping. CellPheno quantifies an entire P4 mouse brain within 15 hours. We showcase whole-brain morphometry, enhanced stitching, and co-localization across multiple cell types in 53 brains.

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Wei, Z., Curtin, I., Kyere, F. A., Borland, D., Yi, H., Kim, M., Dere, M., McCormick, C. M., Krupa, O., Shih, Y.-Y. I., Zylka, M. J., Stein, J. L., Wu, G.. 2026-03-19. CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images. https://doi.org/10.64898/2026.03.17.712391

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