Very tentatively announcing: cellfinder - fully automated 3D cell detection and registration of whole-brain images
It’s at a very early alpha stage, but cellfinder currently:
- Uses a combination of conventional image analysis and deep learning to detect cells with complex morphology in large (up to TB) datasets
- Registers images to an atlas
- Allows analysis/plotting of detected cells/brain regions in standard space
Currently only the Allen Mouse atlas is supported, but we’re looking for anyone willing to test the software, or provide data so we can support more applications.