Tissue clearing combined with light-sheet microscopy is gaining popularity among neuroscientists interested in unbiased assessment of their samples in 3D volume, while the analysis of such data remains a challenge. ClearMap and CellFinder are tools for analysing 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 present application aims to bridge this gap and make the data analysis accessible for a wider scientific community. We developed ClearFinder: an easy-to-adopt graphical user interface (GUI) for cell quantification and group analysis of whole cleared mouse brains. Basic statistical analysis and additional visualization features allow a quick evaluation of the data and establishment of quality checks. Furthermore, we report major differences in total cell counts between CellFinder and ClearMap, when cross-analysing the same samples, underscoring the need for optimizing reproducibility within the field. ClearFinder offers a comprehensive solution tailored for scientists from various disciplines to process whole-brain light-sheet microscopy imaging data efficiently. Key features include: User-friendly interface: ClearFinder provides an intuitive platform for detecting and assigning cells throughout the entire mouse brain volume using the capabilities of the ClearMap and CellFinder toolsRobust installation process: by maintaining independent virtual environments, ClearFinder ensures a robust and standardized installation process, simplifying the setup for usersEnhanced functionality: ClearFinder extends basic processing capabilities by incorporating additional features such as result visualization through heatmap plotting and basic statistical analysis including PCA and box plots.