ClearMap 2: Mapping activity with CellMap

ClearMap 2 is a powerful tool for performing whole-brain analysis, but if you are new to Python, or unfamiliar with troubleshooting tools developed in Python, you will likely run into trouble getting it to work straight out of the box. This series of guides were created to help you get started, from setting up a new Linux workstation for running ClearMap, to going through how to modify the scripts so that you have a useful foundation for performing your own analysis in ClearMap.

After following our previous post, you should have a working installation of ClearMap 2 ready to analyze whole brain data.