Recursive motion correction for 2-photon imaging data, using one or two color channels. Designed as an extension of NoRMCorre by flatironinstitute (https://github.com/flatironinstitute/NoRMCorre).
User settings can be set and saved using the GUI, 'start_iCorre.m' in the main code directory.
| SETTING | VARIABLE NAME | DEFAULT VALUE |
|---|---|---|
| Batch Directory (optional) | "root_dir" | "" |
| Search Filter (optional) | "search_filter" | "" |
| Save Settings As... | "path_settings" | path_settings |
| ScanImage Version | "scim_ver" | 5 |
| Number of Frames to Average for Reference Image | "nFrames_seed" | 1000 |
| Rigid Correction: Max. Number of Repeats | "maxRepRMC" | 1 |
| Non-Rigid Correction: Max. Number of Repeats | "maxRepNRMC" | 1 |
| Rigid Correction: Max. Shift (pixels) | "max_shift" | 10 |
| Non-Rigid Correction: Max. Deviation from Rigid Shift (pixels) | "max_dev" | 5 |
| Non-Rigid Correction: Patch Width | "grid_size" | 16 |
| Error Tolerance (pixels) | "max_err" | 1 |
| Reference Channel (0 for 1-color imaging) | "ref_channel" | 0 |
| Follower Channel (0 for 1-color imaging) | "reg_channel" | 0 |
| Save Concatenated Copy of Corrected Stacks? (T/F) | "do_stitch" | T |
| Downsample Factor for Concatenated Stack | "bin_width" | 20 |
| Delete MAT files at Completion? (T/F) | "delete_mat" | F |