Contrast enhancement and registration

[lauraporta]

Is your feature request related to a problem? Please describe.
Contrast enhancement was applied to the derotated video to improve registration performance. It worked when the optimal thresholds for the contrast were calculated on a frame-by-frame basis. However this introduces a lot of noise and artefacts.

You can see that the background gets more noisy at certain angles, and this is due to the changes in the overall ranges of pixels intensities from frames that are derotated, likely due to un-sampling of certain pixels.

Describe the solution you'd like
I would like to take optimal rigid registration shifts using the contrast enhancement derotated video and apply them to the original one. I could create a custom registration script leveraging suite2p tools.

Describe alternatives you've considered
No contrast enhancement: poor registration with suite2p.
Contrast enhancement with the same thresholds for all the video: poor registration with suite2p.

[lauraporta]

A good starting point seems to be run_s2p.py.

[lauraporta]

The methods I've implemented are actually doing an operation called "clipping".
It's a simple form of contrast enhancement, and there are many others (histogram equalisation, gamma correction, local contrast ehancement, ...).
It would be worth to explore their impact on registration and neuropil subtraction.
Also, it is worth to explore the literature more.

[lauraporta]

Suite2p registration already uses clipping to improve performance. Options file already contains a bool called norm_frames to use this feature. However, as for the current suite2p version, the clipping percentile is hardcoded. See suite2p register_frames method. I can edit it with my preferred percentile.

Thanks @carsen-stringer for the suggestion.