Default SWIM Settings:
Multiprocessing Functions – Fully parallelized, chains of calls to iscale2, MIR, and SWIM
Output Settings – Regenerating the alignment--distinct from computing the alignment--refers to the process of generating a new aligned image stack at a particular scale from source images of the same scale using predetermined affine transformations. The resulting images depend on:
Correcting Misalignment - When Default Grid alignment fails, there are several different options to correct with human-intervention.