Initial release (w/ README markdown)
We developed UNRAVEL (UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images) as a command line tool for voxel-wise analysis of c-Fos immunofluorescence (IF) across the cleared mouse brains and validation of identified clusters of significant voxels using c-Fos+ cell density quantification at cellular resolution.
Please refer to guides regarding necessary dependencies, paths that need to be updated, conventions for file/folder organization and detailed info on running scripts. Key scripts include: find_clusters.sh, glm.sh, and validate_clusters2.sh. Other scripts can be run in a modular fashion (e.g., overview -> prep_tifs.sh -> 488_to_nii.sh -> reg.sh -> rb.sh -> z_brain_template_mask.sh -> glm.sh -> validate_clusters2.sh). Help guides can be found at the beginning of each script or by running: <script>.sh help
If you are unfamiliar with the command line interface, please review Unix tutorials here: https://andysbrainbook.readthedocs.io/en/latest/index.html