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Related Experiment Video

Updated: Mar 28, 2026

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

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

Ziquan Wei¹, Ian Curtin^2,3, Felix A Kyere^2,3

¹Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA.

Biorxiv : the Preprint Server for Biology

|March 27, 2026

Summary

This summary is machine-generated.

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.

Keywords:

3D Nuclei instance segmentation Cellular phenotyping Light-sheet fluorescence microscopy image Machine learning Whole-brain analysis

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Last Updated: Mar 28, 2026

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

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High-resolution Confocal Imaging of the Blood-brain Barrier: Imaging, 3D Reconstruction, and Quantification of Transcytosis

High-resolution Confocal Imaging of the Blood-brain Barrier: Imaging, 3D Reconstruction, and Quantification of Transcytosis

Published on: November 16, 2017

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.