Region-Based Cell Quantification and Visualization in Mouse Brain Atlas Using MATLAB

This dataset provides all necessary resources to replicate voxel-based regional cell quantification in mouse brain atlas space, as described in the associated manuscript. It includes:Annotated brain atlas files in NIfTI format at different resolutions (10 µm, 25 µm, 50 µm), compatible with the Allen Brain Atlas coordinate frameworkJSON-formatted annotation hierarchies, either directly downloaded from the Allen Brain Atlas or manually edited (as provided in Data S1 and Data S2)Voxel coordinate data (CSV format) from processed imaging experimentsMATLAB scripts for mapping voxel coordinates to annotated regions, quantifying region-based signal counts, and visualizing 3D signal distributionREADME files for each script explaining usage and customizationUsers can replace the example CSV with their own voxel data and optionally edit the JSON hierarchy or annotation volume to designate target regions of interest. This platform-independent pipeline enables flexible quantitative analysis across brain regions in cleared tissue or 3D imaging datasets.