adapt spec to RFC-2 revision

ome · Jul 2, 2024 · ee4ce14 · ee4ce14
1 parent 00371a3
commit ee4ce14
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Showing 29 changed files with 250 additions and 119 deletions.
diff --git a/latest/examples/bf2raw/image.json b/latest/examples/bf2raw/image.json
@@ -2,6 +2,6 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": { "bioformats2raw.layout": 3 }
+    "ome": { "version": "0.5", "bioformats2raw.layout": 3 }
   }
 }
diff --git a/latest/examples/bf2raw/plate.json b/latest/examples/bf2raw/plate.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "bioformats2raw.layout": 3,
       "plate": {
         "columns": [

diff --git a/latest/examples/label_strict/colors_properties.json b/latest/examples/label_strict/colors_properties.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "image-label": {
         "colors": [
           {

diff --git a/latest/examples/multiscales_strict/multiscales_example.json b/latest/examples/multiscales_strict/multiscales_example.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "multiscales": [
         {
           "name": "example",

diff --git a/latest/examples/multiscales_strict/multiscales_transformations.json b/latest/examples/multiscales_strict/multiscales_transformations.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "multiscales": [
         {
           "axes": [

diff --git a/latest/examples/ome/series-2.json b/latest/examples/ome/series-2.json
@@ -2,8 +2,6 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
-      "series": ["0", "1"]
-    }
+    "ome": { "version": "0.5", "series": ["0", "1"] }
   }
 }
diff --git a/latest/examples/plate_strict/plate_2wells.json b/latest/examples/plate_strict/plate_2wells.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "plate": {
         "acquisitions": [
           {

diff --git a/latest/examples/plate_strict/plate_6wells.json b/latest/examples/plate_strict/plate_6wells.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "plate": {
         "acquisitions": [
           {

diff --git a/latest/examples/well_strict/well_2fields.json b/latest/examples/well_strict/well_2fields.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "well": {
         "images": [
           {

diff --git a/latest/examples/well_strict/well_4fields.json b/latest/examples/well_strict/well_4fields.json
@@ -2,7 +2,8 @@
   "zarr_format": 3,
   "node_type": "group",
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "well": {
         "images": [
           {

diff --git a/latest/index.bs b/latest/index.bs
@@ -162,13 +162,17 @@ for discovering certain types of data, especially images.
 
 The OME-Zarr Metadata is stored in the various `zarr.json` files throughout the above array
 hierarchy. In this file, the metadata is stored under the namespaced key 
-`https://ngff.openmicroscopy.org/0.5` in `attributes`.
+`ome` in `attributes`.
+The version of the OME-Zarr Metadata is denoted as a string in the `version` attribute within the `ome` namespace.
+
+The OME-Zarr Metadata version MUST be consistent within a hierarchy.
 
 ```json
 {
   ...
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       ...
     }
   }
@@ -402,7 +406,8 @@ labeled multiscale image(s). All label images SHOULD be listed within this metad
 {
   ...
   "attributes": {
-    "https://ngff.openmicroscopy.org/0.5": {
+    "ome": {
+      "version": "0.5",
       "labels": [
         "cell_space_segmentation"
       ]
@@ -609,7 +614,7 @@ Citing {#citing}
 
 [Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4)
 J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022.
-This edition of the specification is [https://ngff.openmicroscopy.org/0.4/](https://ngff.openmicroscopy.org/0.4/]).
+This edition of the specification is [https://ngff.openmicroscopy.org/0.5/](https://ngff.openmicroscopy.org/0.5/]).
 The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/).
 [(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107)
 

diff --git a/latest/schemas/bf2raw.schema b/latest/schemas/bf2raw.schema
@@ -9,7 +9,7 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
@@ -19,15 +19,19 @@
               "enum": [
                 3
               ]
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "bioformats2raw.layout"
+            "bioformats2raw.layout",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },

diff --git a/latest/schemas/image.schema b/latest/schemas/image.schema
@@ -9,7 +9,7 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
@@ -18,15 +18,19 @@
             },
             "omero": {
               "$ref": "#/$defs/omero"
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "multiscales"
+            "multiscales",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },

diff --git a/latest/schemas/label.schema b/latest/schemas/label.schema
@@ -9,21 +9,25 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
             "image-label": {
               "$ref": "#/$defs/image-label"
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "image-label"
+            "image-label",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },

diff --git a/latest/schemas/ome.schema b/latest/schemas/ome.schema
@@ -9,7 +9,7 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
@@ -20,15 +20,19 @@
                 "type": "string"
               },
               "minContains": 1
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "series"
+            "series",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },

diff --git a/latest/schemas/plate.schema b/latest/schemas/plate.schema
@@ -9,7 +9,7 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
@@ -140,15 +140,19 @@
                 "rows",
                 "wells"
               ]
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "plate"
+            "plate",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },

diff --git a/latest/schemas/strict_image.schema b/latest/schemas/strict_image.schema
@@ -8,7 +8,7 @@
       "properties": {
         "attributes": {
           "properties": {
-            "https://ngff.openmicroscopy.org/0.5": {
+            "ome": {
               "properties": {
                 "multiscales": {
                   "items": {

diff --git a/latest/schemas/strict_label.schema b/latest/schemas/strict_label.schema
@@ -8,7 +8,7 @@
       "properties": {
         "attributes": {
           "properties": {
-            "https://ngff.openmicroscopy.org/0.5": {
+            "ome": {
               "properties": {
                 "image-label": {
                   "required": [

diff --git a/latest/schemas/strict_plate.schema b/latest/schemas/strict_plate.schema
@@ -8,7 +8,7 @@
       "properties": {
         "attributes": {
           "properties": {
-            "https://ngff.openmicroscopy.org/0.5": {
+            "ome": {
               "properties": {
                 "plate": {
                   "properties": {

diff --git a/latest/schemas/version.schema b/latest/schemas/version.schema
@@ -0,0 +1,10 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "https://ngff.openmicroscopy.org/latest/schemas/version.schema",
+  "title": "OME-Zarr Metadata version",
+  "description": "The version of the OME-Zarr Metadata",
+  "type": "string",
+  "enum": [
+    "0.5"
+  ]
+}
diff --git a/latest/schemas/well.schema b/latest/schemas/well.schema
@@ -9,7 +9,7 @@
       "description": "The zarr.json attributes key",
       "type": "object",
       "properties": {
-        "https://ngff.openmicroscopy.org/0.5": {
+        "ome": {
           "description": "The versioned OME-Zarr Metadata namespace",
           "type": "object",
           "properties": {
@@ -43,15 +43,19 @@
               "required": [
                 "images"
               ]
+            },
+            "version": {
+              "$ref": "https://ngff.openmicroscopy.org/latest/schemas/version.schema"
             }
           },
           "required": [
-            "well"
+            "well",
+            "version"
           ]
         }
       },
       "required": [
-        "https://ngff.openmicroscopy.org/0.5"
+        "ome"
       ]
     }
   },