A toolbox for quantification and registration of volumetric data from cleared tissue to a reference brain atlas. The toolbox is developed for large light sheet volumetric data from solvent based cleared mouse brain samples. The method is described in ref paper.
Files needed to use the pipeline can be downloaded here: https://www.neuropedia.dk/resource/uncovering-cns-access-of-lipidated-exendin-4-analogues-by-quantitative-whole-brain-3d-light-sheet-imaging/
The pipeline uses Elastix for registration. Elastix binaries can be found here: https://elastix.lumc.nl/download.php