Tools for 2D mouse brain registration to the Allen Common Coordinate Framework (CCF)
Adapted from allenCCF - A comprehensive toolkit for registering histological brain slices to the Allen Brain Atlas and analyzing spatial distributions of cells and regions of interest.
- Automated brain slice registration to Allen CCF coordinates
- Interactive MATLAB GUI for manual registration refinement
- ROI analysis with spatial coordinate extraction
- Batch processing support for whole-brain datasets
- Multiple imaging modalities (fluorescence, DAPI, multi-channel)
- Flexible data structure for various experimental workflows
- please refer to the full documentation
Yu-Ting Wei - [email protected]