PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations

Complex distortions on calcium imaging often impair image registration accuracy. Here, we developed a registration algorithm, PatchWarp, to robustly correct slow image distortion for calcium imaging data. PatchWarp is a two-step algorithm with rigid and non-rigid image registrations. To correct non-uniform image distortions, it splits the imaging field and estimates the best affine transformation matrix for each of the subfields. The distortion-corrected subfields are stitched together like a patchwork to reconstruct the distortion-corrected imaging field. We show that PatchWarp robustly corrects image distortions of calcium imaging data collected from various cortical areas through glass window or gradient-index (GRIN) lens with a higher accuracy than existing non-rigid algorithms. Furthermore, it provides a fully automated method of registering images from different imaging sessions for longitudinal neural activity analyses. PatchWarp improves the quality of neural activity analyses and is useful as a general approach to correct image distortions in a wide range of disciplines.