State of ophys processing pipeline

# Registration
- Using suite2p nonrigid registration
- Nonrigid registration parameter is not validated
- [ ] Develop QC protocol for nonrigid registration
- Structural similarity between the first, middle, and the last episodic mean FOVs
- Manual visualization with scroll (and/or toggle).
# Decrosstalk
- Using grid search for minimum mutual information
# ROI segmentation
- CellPose on the mean image (for now)
- [ ] Develop QC protocol for cell segmentation
- ROI boundary overlaid on top of mean / enhanced mean / max image
# Neuropil correction
- Using grid search for minimum mutual information
- [ ] Develop QC protocol
# Demixing
- [ ] Quantify ROI overlap with z-drift
- Question: how much of the ROI overlap is due to z-drift? (i.e., how much ROI overlap is due to axial PSF of 2p?)
# Cell to cell matching
- Currently using rigid registration between sessions
- Not optimal since we now use nonrigid registration within a session
- [ ] Develop QC protocol
# Data Assessment (tentative)
- Manual curation on the data quality (good for further analysis)
- Excel sheet
- [ ] For GCaMP pilot data so far (2024/01/22)
- Laser issue, seizure, etc.
- [ ] For LAMF data
# QC capsule
## z-drift
# Documentation