gin commit from h-laptop

New files: 188

segmentation_datasets/minian/README.md

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+## 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`

segmentation_datasets/minian/segmented_data_3units_100frames/.zgroup

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+{
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/A/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        1,
+        304,
+        304
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f8",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3,
+        608,
+        608
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/A/.zattrs

@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id",
+        "height",
+        "width"
+    ],
+    "coordinates": "animal session_id session"
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/animal/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U7",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/animal/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/height/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        608
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        608
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/height/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "height"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/session/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U14",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/session/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/session_id/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U9",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/session_id/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/unit_id/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/unit_id/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/width/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        608
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        608
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/A.zarr/width/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "width"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/C/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        3,
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f8",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3,
+        100
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/C/.zattrs

@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id",
+        "frame"
+    ],
+    "coordinates": "animal session_id session"
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/animal/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U7",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/animal/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/frame/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        100
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/frame/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "frame"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/session/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U14",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/session/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/session_id/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U9",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/session_id/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/unit_id/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/C.zarr/unit_id/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/S/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        3,
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f8",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3,
+        100
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/S/.zattrs

@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id",
+        "frame"
+    ],
+    "coordinates": "animal session_id session"
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/animal/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U7",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/animal/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/frame/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        100
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        100
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/frame/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "frame"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/session/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U14",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/session/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/session_id/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U9",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/session_id/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/unit_id/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        3
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/S.zarr/unit_id/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "unit_id"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/.zattrs

@@ -0,0 +1,3 @@
+{
+    "coordinates": "animal session_id session"
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/animal/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U7",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/animal/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/b/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        152,
+        304
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f8",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        608,
+        608
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/b/.zattrs

@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "height",
+        "width"
+    ],
+    "coordinates": "unit_id"
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/height/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        608
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        608
+    ],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/height/.zattrs

@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "height"
+    ]
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/session/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U14",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/session/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/session_id/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<U9",
+    "fill_value": "",
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/session_id/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/unit_id/.zarray

@@ -0,0 +1,10 @@
+{
+    "chunks": [],
+    "compressor": null,
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [],
+    "zarr_format": 2
+}

segmentation_datasets/minian/segmented_data_3units_100frames/b.zarr/unit_id/.zattrs

@@ -0,0 +1,3 @@
+{
+    "_ARRAY_DIMENSIONS": []
+}