Changes to the spec and schemata for RFC-2

.github/workflows/publish.yml

@@ -12,10 +12,10 @@ on:
 jobs:
   main:
     name: Build, Validate and Deploy
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v2
-      - uses: ome/spec-prod@main
+      - uses: normanrz/spec-prod@patch-1
         with:
           GH_PAGES_BRANCH: gh-pages
           VALIDATE_LINKS: false

.github/workflows/validation.yml

@@ -14,6 +14,7 @@ jobs:
           - '0.2'
           - '0.3'
           - '0.4'
+          - '0.5'
           - 'latest'
     runs-on: ubuntu-20.04
     steps:

.readthedocs.yaml

@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.10"
 

0.1/index.bs

@@ -3,7 +3,6 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
 URL: https://ngff.openmicroscopy.org/0.1/
 Repository: https://github.com/ome/ngff
 Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff

0.2/index.bs

@@ -3,7 +3,6 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
 URL: https://ngff.openmicroscopy.org/0.2/
 Repository: https://github.com/ome/ngff
 Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff

0.3/index.bs

@@ -3,7 +3,6 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
 URL: https://ngff.openmicroscopy.org/0.3/
 Repository: https://github.com/ome/ngff
 Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff

0.4/index.bs

@@ -4,7 +4,6 @@ Shortname: ome-ngff
 Level: 1
 Status: LS-COMMIT
 Status: w3c/CG-FINAL
-Group: ome
 URL: https://ngff.openmicroscopy.org/0.4/
 Repository: https://github.com/ome/ngff
 Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff

0.5/examples/bf2raw/image.json

@@ -0,0 +1,10 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "bioformats2raw.layout": 3
+    }
+  }
+}

0.5/examples/bf2raw/plate.json

@@ -0,0 +1,36 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "bioformats2raw.layout": 3,
+      "plate": {
+        "columns": [
+          {
+            "name": "1"
+          }
+        ],
+        "name": "Plate Name 0",
+        "wells": [
+          {
+            "path": "A/1",
+            "rowIndex": 0,
+            "columnIndex": 0
+          }
+        ],
+        "field_count": 1,
+        "rows": [
+          {
+            "name": "A"
+          }
+        ],
+        "acquisitions": [
+          {
+            "id": 0
+          }
+        ]
+      }
+    }
+  }
+}

0.5/examples/label_strict/colors_properties.json

@@ -0,0 +1,37 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "image-label": {
+        "colors": [
+          {
+            "label-value": 0,
+            "rgba": [0, 0, 128, 128]
+          },
+          {
+            "label-value": 1,
+            "rgba": [0, 128, 0, 128]
+          }
+        ],
+        "properties": [
+          {
+            "label-value": 0,
+            "area (pixels)": 1200,
+            "class": "intercellular space"
+          },
+          {
+            "label-value": 1,
+            "area (pixels)": 1650,
+            "class": "cell",
+            "cell type": "neuron"
+          }
+        ],
+        "source": {
+          "image": "../../"
+        }
+      }
+    }
+  }
+}

0.5/examples/multiscales_strict/multiscales_example.json

@@ -0,0 +1,68 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "multiscales": [
+        {
+          "name": "example",
+          "axes": [
+            { "name": "t", "type": "time", "unit": "millisecond" },
+            { "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": [
+                {
+                  // the voxel size for the first scale level (0.5 micrometer)
+                  "type": "scale",
+                  "scale": [1.0, 1.0, 0.5, 0.5, 0.5]
+                }
+              ]
+            },
+            {
+              "path": "1",
+              "coordinateTransformations": [
+                {
+                  // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
+                  "type": "scale",
+                  "scale": [1.0, 1.0, 1.0, 1.0, 1.0]
+                }
+              ]
+            },
+            {
+              "path": "2",
+              "coordinateTransformations": [
+                {
+                  // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
+                  "type": "scale",
+                  "scale": [1.0, 1.0, 2.0, 2.0, 2.0]
+                }
+              ]
+            }
+          ],
+          "coordinateTransformations": [
+            {
+              // the time unit (0.1 milliseconds), which is the same for each scale level
+              "type": "scale",
+              "scale": [0.1, 1.0, 1.0, 1.0, 1.0]
+            }
+          ],
+          "type": "gaussian",
+          "metadata": {
+            "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
+            "method": "skimage.transform.pyramid_gaussian",
+            "version": "0.16.1",
+            "args": "[true]",
+            "kwargs": { "multichannel": true }
+          }
+        }
+      ]
+    }
+  }
+}

0.5/examples/multiscales_strict/multiscales_transformations.json

@@ -0,0 +1,47 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "multiscales": [
+        {
+          "axes": [
+            {
+              "name": "y",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "x",
+              "type": "space",
+              "unit": "micrometer"
+            }
+          ],
+          "datasets": [
+            {
+              "path": "0",
+              "coordinateTransformations": [
+                {
+                  "scale": [1, 1],
+                  "type": "scale"
+                }
+              ]
+            }
+          ],
+          "coordinateTransformations": [
+            {
+              "scale": [10, 10],
+              "type": "scale"
+            }
+          ],
+          "name": "image_with_coordinateTransformations",
+          "type": "foo",
+          "metadata": {
+            "key": "value"
+          }
+        }
+      ]
+    }
+  }
+}

0.5/examples/ome/series-2.json

@@ -0,0 +1,10 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "series": ["0", "1"]
+    }
+  }
+}

0.5/examples/plate_strict/plate_2wells.json

@@ -0,0 +1,97 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "plate": {
+        "acquisitions": [
+          {
+            "id": 1,
+            "maximumfieldcount": 1,
+            "name": "single acquisition",
+            "starttime": 1343731272000
+          }
+        ],
+        "columns": [
+          {
+            "name": "1"
+          },
+          {
+            "name": "2"
+          },
+          {
+            "name": "3"
+          },
+          {
+            "name": "4"
+          },
+          {
+            "name": "5"
+          },
+          {
+            "name": "6"
+          },
+          {
+            "name": "7"
+          },
+          {
+            "name": "8"
+          },
+          {
+            "name": "9"
+          },
+          {
+            "name": "10"
+          },
+          {
+            "name": "11"
+          },
+          {
+            "name": "12"
+          }
+        ],
+        "field_count": 1,
+        "name": "sparse test",
+        "rows": [
+          {
+            "name": "A"
+          },
+          {
+            "name": "B"
+          },
+          {
+            "name": "C"
+          },
+          {
+            "name": "D"
+          },
+          {
+            "name": "E"
+          },
+          {
+            "name": "F"
+          },
+          {
+            "name": "G"
+          },
+          {
+            "name": "H"
+          }
+        ],
+        "wells": [
+          {
+            "path": "C/5",
+            "rowIndex": 2,
+            "columnIndex": 4
+          },
+          {
+            "path": "D/7",
+            "rowIndex": 3,
+            "columnIndex": 6
+          }
+        ]
+      }
+    }
+  }
+}