Motion Correction

After downsampling, correct motion artifacts in each session.

Use:

CaliAli_options = CaliAli_motion_correction(CaliAli_options);

Output File

This step creates *_mc.mat files. For naming and save-location details, see FAQ output naming.

Important

Ensure to visually inspect the motion-corrected video before proceeding to the next step: view_Ca_video()

Limitations of the non-rigid registration module

This code is experimental and may introduce undesired deformations when adjusting for non-rigid deformation.

How long it takes to motion correct videos?

Rigid: processes ~5,000 frames in about 2 minutes on a modern CPU.
Non-rigid: substantially slower at roughly 10 frames per second.

Crop after motion correction

Use CaliAli_crop() to interactively draw a shared region of interest across the motion-corrected sessions. The tool opens representative frames, lets you define the final field of view, and rewrites each _mc file in-place so downstream detrending and alignment run on the trimmed data.