Motion correction (rigid and piecewise rigid)

Motion correction is a necessary first step in the calcium imaging data analysis pipeline. CaImAn uses the NoRMCorre algorithm for performing fast rigid or piecewise rigid motion correction.

For a demo you can run the notebook demo_motion_correction.ipynb which can be found in your demos/notebooks folder.

More information about the algorithm can be found in the paper:

Pnevmatikakis, E.A., and Giovannucci A. (2017). NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data. Journal of Neuroscience Methods, 291:83-92 [paper]