Calcium imaging registration pipeline, a rewrite of the Suite2p approach in Julia, and extended to 3D.
Pipelines for common calcium imaging use cases are provided, but individual functions can be mixed and applied in different ways for other cases.
- reference creation:
make_reference
To align individual or small stacks
- translation-only registration:
find_translationandtranslate - non-rigid piecewise-translation registration:
find_deformation_mapandapply_deformation_map
To align large datasets that do not fit in memory:
- for volumetric data (e.g. lightsheet)
register_volumes! - for planar data (e.g. two-photon)
make_planar_referenceandregister_planewise!
shift = find_translation(moving, reference)
corrected = translate(moving, shift)