CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images
Ziquan WeiiD, Ian CurtiniD, Felix A. KyereiD, David BorlandiD, Hong YiiD, Minjeong KimiD, Mustafa DereiD, Carolyn M. McCormick, Oleh Krupa, Yen‐Yu Ian ShihiD, Mark J. ZylkaiD, Jason L. SteiniD, Guorong Wu AiD
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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