ophys_testing_data/segmentation_datasets/minian/README.md

Files provided by Cai Lab

The directory named segmented_data_3units_100frames contains a stub version of data provided by the Cai Lab to test minian segmentation interface.

The data contains timeStamps.csv file with 'Frame Number' and 'Time Stamp (ms)' headers, and a .zarr dataset with the following structure:

minian/
├── A.zarr 
│   ├── A (3, 608, 608) float64
│   ├── animal () <U7
│   ├── height (608,) int64
│   ├── session_id () <U9
│   ├── unit_id (3,) int64
│   └── width (608,) int64
├── C.zarr
│   ├── C (3, 100) float64
│   ├── animal () <U7
│   ├── frame (100,) int64
│   ├── session () <U14
│   └── session_id () <U9
│   └── unit_id (3,) 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 (3, 100) float64
│   ├── frame (100,) int64
│   ├── session () <U14
│   ├── session_id () <U9
│   └── unit_id (3,) int64
├── c0.zarr
│   ├── animal () <U7
│   ├── c0 (3, 100) float64
│   ├── frame (100,) int64
│   └── session () <U14
├── f.zarr
│   ├── animal () <U7
│   ├── f (100,) float64
│   └── frame (100,) int64
├── S.zarr
│   ├── S (3, 100) float64
│   ├── animal () <U7
│   ├── frame (100,) int64
│   ├── session () <U14
│   └── session_id () <U9
│   └── unit_id (3,) 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