ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues.

ClearMap is targeted towards large lightsheet volumetric imaging data of iDISCO+ cleared mouse brains samples, their registration to the Allen brain atlas, volumetric image processing and statistical analysis.

The method is fully described in this Cell paper. For further details visit the iDISCO website and the ClearMap documentation.

Install ClearMap by cloning it form github:

$ git clone https://github.com/ChristophKirst/ClearMap.git

See GIT.md for basic help with git.

If you want to register data to reference images via elastix or classify pixels via ilastik configure the /ClearMap/Settings.py file.

You will most likely also need to install several python packages e.g. via pip or apt-get.

See the documentation for more details.

Additional files for mouse brain registration can be found on the iDISCO website.

• see the template scripts in the ./ClearMap/Scripts folder
• see the ClearMap documentation

(c) 2016 Christoph Kirst The Rockefeller University, [email protected]

GPLv3, see LICENSE.txt for details.