ClearFinder: a Python GUI for annotating cells in cleared mouse brain

Abstract

BackgroundTissue clearing combined with light-sheet microscopy is gaining popularity among neuroscientists interested in unbiased assessment of their samples in 3D volume. However, the analysis of such data remains a challenge. ClearMap and CellFinder are tools for analyzing neuronal activity maps in an intact volume of cleared mouse brains. However, these tools lack a user interface, restricting accessibility primarily to scientists proficient in advanced Python programming. The application presented here aims to bridge this gap and make data analysis accessible to a wider scientific community.ResultsWe developed an easy-to-adopt graphical user interface for cell quantification and group analysis of whole-cleared adult mouse brains. Fundamental statistical analysis, such as PCA and box plots, and additional visualization features allow for quick data evaluation and quality checks. Furthermore, we report significant differences in total cell counts between CellFinder and ClearMap when cross-analyzing the same samples, underscoring the need for optimizing reproducibility within the field.ConclusionsOur easily accessible tool allows more researchers to implement the methodology, troubleshoot arising issues, and develop quality checks, benchmarking, and standardized analysis pipelines for cell detection and region annotation in whole volumes of cleared brains.