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Updated: Mar 28, 2026
Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy
Published on: August 1, 2022
CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images
Ziquan Wei1, Ian Curtin2,3, Felix A Kyere2,3
1Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA.
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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