Python code: Lightsheet Alignment
Output Details
Description
Python scripts used to align a moving light-sheet specimen to a fixed reference through their autofluorescence (AF) channels. Marker channels are not registered independently: the AF-derived transform is applied unchanged. Steps of this light-sheet inter-specimen registration pipeline include 1) convert fixed AF HDF5 from DV,AP,LR to an isotropic AP,DV,LR registration grid, 2) extract selected IMS channels and create isotropic registration volumes, 3) estimate affine plus SyN registration and apply it to all moving channels, 4) test a conservative rigid correction in a user-defined ROI and accept it only when prespecified QC criteria improve, 5) compose saved transforms and sample the original Level-0 IMS signal in fixed space, and 6) calculate whole-volume and ROI metrics and create registration overlays.
Identifier (DOI)
10.5281/zenodo.23017722
