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Updated: Mar 28, 2026
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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.
CellPheno is a new framework for efficient 3D whole-brain analysis. It enables high-throughput cellular phenotyping and morphometry in mouse brains, significantly improving quantification speed.
Area of Science:
- Neuroscience
- Biotechnology
- Computational Biology
Background:
- Tissue clearing and light-sheet microscopy allow for high-resolution 3D whole-brain imaging.
- Current whole-brain quantification tools lack efficiency and comprehensive morphometric assessment.
Purpose of the Study:
- To introduce CellPheno, a novel 3D nuclei instance segmentation framework.
- To enable high-throughput cellular phenotyping and whole-brain morphometry.
Main Methods:
- Development of CellPheno, a 3D nuclei instance segmentation framework.
- Application of CellPheno to P4 mouse brains for quantification and morphometry.
- Analysis of 53 mouse brains to showcase capabilities.
Main Results:
- CellPheno quantifies an entire P4 mouse brain in under 15 hours.
- Demonstration of whole-brain morphometry and enhanced stitching.
- Successful co-localization analysis across multiple cell types.
Conclusions:
- CellPheno provides an efficient solution for high-throughput cellular phenotyping in whole brains.
- The framework advances the analysis of large-scale 3D neuroimaging data.
- Enables comprehensive studies of brain morphometry and cell type distribution.
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