Anyone analysing whole-brain images? E.g. cleared tissue, serial two-photon?

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.

If you have any questions please get in touch on here, via github or via email.


Now with a few more details of how it works here.

If you’re going to NEUBIAS next month and fancy a chat, let me know.


Cellfinder version 0.3.12 released with full Windows & Linux support.

pip install cellfinder --upgrade to try it out.

More details at