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.

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.