LightsheetRegistration.ipynb provides an example workflow for multistage registration of SmartSPIM data to the Allen Institute Common Coordinate Framework (CCF) atlas.
Current Behavior
The lightsheet example notebook evaluates registration results via the voxel difference image between the resampled moving image and the fixed image. Since registration is cross-modal, we expect large voxel differences, so it is difficult to know how far the registration result is from a "perfect" registration.
Request Behavior
The Allen Institute has annotated the 652506 SmartSPIM sample and the CCF atlas with point landmarks. We should evaluate registration results as follows:
Transform SmartSPIM landmarks by the output forward transform from registration
Compute distance statistics between the transformed SmartSPIM landmarks and reference CCF atlas.
Background
LightsheetRegistration.ipynb provides an example workflow for multistage registration of SmartSPIM data to the Allen Institute Common Coordinate Framework (CCF) atlas.
Current Behavior
The lightsheet example notebook evaluates registration results via the voxel difference image between the resampled moving image and the fixed image. Since registration is cross-modal, we expect large voxel differences, so it is difficult to know how far the registration result is from a "perfect" registration.
Request Behavior
The Allen Institute has annotated the 652506 SmartSPIM sample and the CCF atlas with point landmarks. We should evaluate registration results as follows: