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.
❗ 💣 Note 💣 ❗
This is ClearMap 1.0.
ClearMap 2.0 with WobblyStitcher and TubeMap for our 2020 Cell paper can be found under
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.
(c) 2016 Christoph Kirst The Rockefeller University, firstname.lastname@example.org
GPLv3, see LICENSE.txt for details.