Whole-brain microscopy image analysis

I’m developing tools for the analysis and visualisation of whole-brain microscopy images. This includes:

  • cellfinder for 3D cell detection (paper)
  • brainreg for 3D registration and atlas-based segmentation
  • brainreg-segment for segmentation and analysis of bulk structures (e.g. Neuropixels probes, injection sites)

For 3D visualisation, I’ve also contributed to Federico Claudi’s excellent brainrender (paper).

These tools are all implemented within the BrainGlobe suite of computational neuroanatomy tools

If you’re interested in whole-brain microscopy image analysis challenges, see the review we wrote.