Whole-organ optical-imaging techniques have paved the way for anatomical studies of the entire central nervous system with single cell resolution. Coupled with tissue clearing and immunolabeling, immediate early gene expression or viral tracings, these techniques have opened the door to a new world of experiments in various biological fields: cancer research, developmental biology or neurosciences. While these techniques provide structural and functional information of entire organs or even entire organisms far more complete than that of conventional 2D histology, and various microscopes have become readily available, the tissue preparation and subsequent data analysis does not rest on commercial kits and software but still relies on expertise and software under active development. During this workshop, we propose to demystify this kind of experiments by showcasing 2 state of the art techniques in the field: • whole brain tissue clearing and labeling using iDISCO • whole brain data analysis using the ClearMap2 open-source software. We will apply the iDISCO method to map brain activity by using a cellular marker of neuronal activity: c-Fos. The 3D scans will then be processed through the ClearMap2 pipeline to align the sample brain to the Allen Brain Atlas and automatically detect the labeled cells. We will finally compare the cell counts between regions and across experimental conditions. The software offers a simple graphical user interface with the aim to empower the end users to analyse their own datasets. Our workshop is intended for anyone interested in studying cells of interest in entire mouse brains, from complete beginners to participants already familiar with clearing techniques but lacking experience pertaining to the quantification. Although we chose to present c-Fos, the techniques presented are applicable to other scientific questions such as the analysis of microglia activation, amyloids plaques, blood vessels or neuronanal connectivity.