Announcing new (ish) tools for whole-brain microscopy atlas registration & segmentation: brainreg & brainreg-segment

These tools have been available for months, but not “officially” released. Today we uploaded the preprint describing:

  • brainreg - Multi-atlas, Python-based registration pipeline for whole-brain microscopy data.
  • brainreg-segment - Napari plugin to segment and analyse the anatomical location of brain regions, lesions and implanted devices (e.g. optical fibres, Neuropixels probes etc.).

Tools like this have been around for years, but the aim of these packages is to simplify brain registration, using multiple atlases, and analysing bulk structures in the brain (rather than individually labelled cells etc).

Documentation, tutorials and example data can be found here.

Get in touch if you have any questions!

Overview of the registration, analysis and visualisation pipeline