MATLAB toolbox for viewing, aligning Allen CCF mouse atlas, and annotating slice histology images.
Inspiration from SHARP-Track by Philip Shamash (https://www.biorxiv.org/content/10.1101/447995v1).
- download the Allen CCF mouse atlas download here *
- clone this repository
- add both the CCF mouse atlas and repository to the matlab path
- The npy-matlab repository
*(note on where these files came from: they are a re-formatted version of the original atlas, which has been processed with this script)
See the wiki for instructions on use
Please raise a GitHub Issue for any problems or questions
2026-02-23 - v2 released. Saved files before this point are incompatible - to use old files, use repo before this date.
2024-02-16 - Split re-order/flip GUIs: re-ordering is now a simpler click interface
2023-11-02 - Created menu GUI for easier interfacing re-structured/improve much of the code, improved auto-align