Add Minian segmentation extractor

[alessandratrapani]

Add segmentation extractor for Minian output. Supported output format: Zarr (for now) Similarly to Caiman uses CNMF to perform cell identification.

Output structure (example):

minian/
 ├── A.zarr 
 │   ├── A (851, 608, 608) float64
 │   ├── animal () <U7
 │   ├── height (608,) int64
 │   ├── session_id () <U9
 │   ├── unit_id (851,) int64
 │   └── width (608,) int64
 ├── C.zarr
 │   ├── C (851, 8931) float64
 │   ├── animal () <U7
 │   ├── frame (8931,) int64
 │   ├── session () <U14
 │   └── session_id () <U9
 │   └── unit_id (851,) int64
 ├── b.zarr
 │   ├── animal () <U7
 │   ├── b (608, 608) float64
 │   ├── height (608,) int64
 │   ├── session () <U14
 │   ├── session_id () <U9
 │   ├── unit_id () int64
 │   └── width (608,) int64
 ├── b0.zarr
 │   ├── animal () <U7
 │   ├── b0 (851, 8931) float64
 │   ├── frame (8931,) int64
 │   ├── session () <U14
 │   ├── session_id () <U9
 │   └── unit_id (851,) int64
 ├── c0.zarr
 │   ├── animal () <U7
 │   ├── c0 (851, 8931) float64
 │   ├── frame (8931,) int64
 │   └── session () <U14
 ├── f.zarr
 │   ├── animal () <U7
 │   ├── f (8931,) float64
 │   └── frame (8931,) int64
 ├── S.zarr
 │   ├── S (851, 8931) float64
 │   ├── animal () <U7
 │   ├── frame (8931,) int64
 │   ├── session () <U14
 │   └── session_id () <U9
 │   └── unit_id (851,) int64
 ├── max_proj.zarr
 │   ├── animal () <U7
 │   ├── max_proj (608, 608) float64
 │   ├── height (608,) int64
 │   ├── session () <U14
 │   ├── session_id () <U9
 │   └── width (608,) int64

• A: Spatial footprints of cells. Should have dimensions (“unit_id”, “height”, “width”). --> image_masks
• C: Temporal components of cells. Should have dimensions “frame” and “unit_id”. --> roi_response_denoised
• b: Spatial footprint of background. Should have dimensions (“height”, “width”). --> background_image_masks
• f: Temporal dynamic of background. Should have dimension “frame”. --> roi_response_neuropil
• b0: Baseline fluorescence for each cell. Should have dimensions (“frame”, “unit_id”) and same shape as C --> roi_response_baseline
• c0: Initial calcium decay, in theory triggered by calcium events happened before the recording starts. Should have dimensions (“frame”, “unit_id”) and same shape as C
• S: Deconvolved spikes for each cell. Should have dimensions (“frame”, “unit_id”) and same shape as C --> roi_response_deconvolved
• max_proj: the maximum projection --> summary_image

TODOs

• [x] add extractor
• [x] update CHANGELOG
• [x] implement tests

[h-mayorquin]

Do tag me when this is ready for review.

[alessandratrapani]

I am uploading on the s3 bucket the testing folder for the minian segmentation data

[alessandratrapani]

@h-mayorquin ready for review

[h-mayorquin]

What's the status of this?