Add files using upload-large-folder tool

annotations_filtered.zarr/.zattrs

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annotations_filtered.zarr/.zgroup

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+}

annotations_filtered.zarr/.zmetadata

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annotations_filtered.zarr/obs/fov_name/.zattrs

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annotations_filtered.zarr/obs/fov_name/.zgroup

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annotations_filtered.zarr/obs/fov_name/categories/.zarray

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annotations_filtered.zarr/obs/fov_name/categories/.zattrs

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annotations_filtered.zarr/obs/fov_name/codes/.zarray

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annotations_filtered.zarr/obs/id/.zarray

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annotations_filtered.zarr/obs/id/.zattrs

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annotations_filtered.zarr/obs/infection_status/.zattrs

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annotations_filtered.zarr/obs/infection_status/.zgroup

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annotations_filtered.zarr/obs/parent_id/.zarray

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annotations_filtered.zarr/obs/parent_id/.zattrs

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annotations_filtered.zarr/obs/parent_track_id/.zarray

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annotations_filtered.zarr/obs/t/.zarray

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annotations_filtered.zarr/obs/t/.zattrs

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annotations_filtered.zarr/obs/track_id/.zarray

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annotations_filtered.zarr/obs/track_id/.zattrs

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annotations_filtered.zarr/obs/x/.zarray

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annotations_filtered.zarr/obs/x/.zattrs

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annotations_filtered.zarr/obs/y/.zarray

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dataset.zarr/A/1/000000/zarr.json

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dataset.zarr/A/1/zarr.json

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dataset.zarr/A/2/000000/0/zarr.json

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dataset.zarr/A/2/000000/zarr.json

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dataset.zarr/A/2/000001/0/zarr.json

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dataset.zarr/A/2/000001/zarr.json

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dataset.zarr/A/2/001000/0/zarr.json

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dataset.zarr/A/2/001000/zarr.json

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dataset.zarr/A/2/001001/0/zarr.json

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dataset.zarr/A/2/001001/zarr.json

@@ -0,0 +1,114 @@
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dataset.zarr/A/2/002000/0/zarr.json

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dataset.zarr/A/2/002000/zarr.json

@@ -0,0 +1,114 @@
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dataset.zarr/A/2/002001/0/zarr.json

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dataset.zarr/A/2/002001/zarr.json

@@ -0,0 +1,114 @@
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+              "name": "C",
+              "type": "channel"
+            },
+            {
+              "name": "Z",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "Y",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "X",
+              "type": "space",
+              "unit": "micrometer"
+            }
+          ],
+          "datasets": [
+            {
+              "path": "0",
+              "coordinateTransformations": [
+                {
+                  "type": "scale",
+                  "scale": [
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+                    1.0,
+                    1.0,
+                    0.1494,
+                    0.1494
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+          "name": "0"
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+      "omero": {
+        "version": "0.5",
+        "id": 0,
+        "name": "002001",
+        "channels": [
+          {
+            "active": true,
+            "coefficient": 1.0,
+            "color": "FFFFFF",
+            "family": "linear",
+            "inverted": false,
+            "label": "Phase3D",
+            "window": {
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+              "end": 0.2,
+              "min": -10.0,
+              "max": 10.0
+            }
+          },
+          {
+            "active": true,
+            "coefficient": 1.0,
+            "color": "00FF00",
+            "family": "linear",
+            "inverted": false,
+            "label": "raw GFP EX488 EM525-45",
+            "window": {
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+              "end": 65535.0,
+              "min": 0.0,
+              "max": 65535.0
+            }
+          },
+          {
+            "active": true,
+            "coefficient": 1.0,
+            "color": "FF00FF",
+            "family": "linear",
+            "inverted": false,
+            "label": "raw mCherry EX561 EM600-37",
+            "window": {
+              "start": 0.0,
+              "end": 65535.0,
+              "min": 0.0,
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+        "rdefs": {
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+          "defaultZ": 0,
+          "model": "color",
+          "projection": "normal"
+        }
+      },
+      "version": "0.5"
+    },
+    "extra_metadata": null
+  },
+  "zarr_format": 3,
+  "node_type": "group"
+}

dataset.zarr/A/2/zarr.json

@@ -0,0 +1,38 @@
+{
+  "attributes": {
+    "ome": {
+      "well": {
+        "version": "0.5",
+        "images": [
+          {
+            "acquisition": 0,
+            "path": "000000"
+          },
+          {
+            "acquisition": 0,
+            "path": "000001"
+          },
+          {
+            "acquisition": 0,
+            "path": "001000"
+          },
+          {
+            "acquisition": 0,
+            "path": "001001"
+          },
+          {
+            "acquisition": 0,
+            "path": "002000"
+          },
+          {
+            "acquisition": 0,
+            "path": "002001"
+          }
+        ]
+      },
+      "version": "0.5"
+    }
+  },
+  "zarr_format": 3,
+  "node_type": "group"
+}

dataset.zarr/A/zarr.json

@@ -0,0 +1,5 @@
+{
+  "attributes": {},
+  "zarr_format": 3,
+  "node_type": "group"
+}

dataset.zarr/zarr.json

@@ -0,0 +1,42 @@
+{
+  "attributes": {
+    "ome": {
+      "plate": {
+        "version": "0.5",
+        "acquisitions": [
+          {
+            "id": 0
+          }
+        ],
+        "rows": [
+          {
+            "name": "A"
+          }
+        ],
+        "columns": [
+          {
+            "name": "1"
+          },
+          {
+            "name": "2"
+          }
+        ],
+        "wells": [
+          {
+            "path": "A/1",
+            "rowIndex": 0,
+            "columnIndex": 0
+          },
+          {
+            "path": "A/2",
+            "rowIndex": 0,
+            "columnIndex": 1
+          }
+        ]
+      },
+      "version": "0.5"
+    }
+  },
+  "zarr_format": 3,
+  "node_type": "group"
+}

infection_transitions_analysis.csv

@@ -0,0 +1,27 @@
+track_id,fov_name,transition_type,n_timepoints,n_uninfected,n_infected,n_unknown,first_timepoint,last_timepoint,first_uninfected_t,first_infected_t,status_sequence
+15,A/2/001001,uninfected→infected,6,1,5,0,38,43,38,39,uni→inf→inf→inf→inf→inf
+42,A/2/001000,uninfected→infected,26,3,23,0,37,62,37,40,uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+93,A/2/000000,uninfected→infected,14,12,2,0,14,41,14,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf
+104,A/2/000001,uninfected→infected,27,19,8,0,20,46,20,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf
+107,A/2/000001,uninfected→infected,46,19,27,0,20,65,20,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+114,A/2/001000,uninfected→infected,49,29,20,0,11,59,11,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+116,A/2/001000,uninfected→infected,30,10,20,0,19,59,19,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+117,A/2/001000,uninfected→infected,47,21,26,0,19,65,19,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+119,A/2/000001,uninfected→infected,27,17,10,0,23,49,23,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+121,A/2/000001,uninfected→infected,28,1,27,0,38,65,38,39,uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+122,A/2/000001,uninfected→infected,28,1,27,0,38,65,38,39,uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+122,A/2/001000,uninfected→infected,26,7,19,0,25,65,25,47,uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+127,A/2/001001,uninfected→infected,29,17,12,0,22,50,22,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+128,A/2/000000,uninfected→infected,36,26,10,0,14,49,14,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+131,A/2/000001,uninfected→infected,2,1,1,0,38,39,38,39,uni→inf
+135,A/2/000000,uninfected→infected,46,36,10,0,4,49,4,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+137,A/2/000001,uninfected→infected,45,39,6,0,0,44,0,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf
+152,A/2/000001,uninfected→infected,64,38,26,0,0,65,0,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+168,A/2/000001,uninfected→infected,38,11,27,0,28,65,28,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+182,A/2/000000,uninfected→infected,55,33,22,0,7,61,7,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+198,A/2/002001,uninfected→infected,23,22,1,0,17,39,17,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf
+205,A/2/000000,uninfected→infected,32,6,26,0,34,65,34,40,uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+209,A/2/000000,uninfected→infected,31,5,26,0,35,65,35,40,uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+210,A/2/002001,uninfected→infected,29,27,2,0,12,40,12,39,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf
+225,A/2/001000,uninfected→infected,40,24,16,0,16,55,16,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf
+240,A/2/001000,uninfected→infected,48,34,14,0,6,53,6,40,uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→uni→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf→inf