BrainGlobe general-purpose registration tool

[adamltyson]

This issue is to start listing features and plans for a general purpose BrainGlobe registration tool. We can discuss here, and then priorities features, turning these into issues and milestones.

Scientific requirements

• Registration of any brain subvolume, including:
  • 2D sections (any orientation, inc some damage)
  • Whole brains
  • Thick sections (e.g. from tissue clearing, acute recordings)
  • Small blocks (e.g. from tissue clearing or expansion microscopy)

Tech requirements

• Python-based (compatibility with BrainGlobe & other bioimage analysis tools)
• Includes a napari plugin for pre-processing and compatibility with BrainGlobe ecosystem
• Registration using elastix (likely itk-elastix) due to community support and existing parameter sets
• Includes default preprocessing options (e.g. using scikit-image)
• Registers to any BrainGlobe atlas
• Compatible with downstream BrainGlobe tools (brainreg-segment, cellfinder etc)
• Compatible with other napari plugins
• Can be automated

Potential steps

• Flexible interface to allow:

  • Data preprocessing
  • Appropriate atlas cropping
  • Running registration
  • Saving results

  Mockup

cc @alessandrofelder @raacampbell @viktorpm

[adamltyson]

Some existing tools in this space