Changes to the spec and schemata for RFC-2

latest/examples/bf2raw/image.json

@@ -1,3 +1,7 @@
 {
-  "bioformats2raw.layout" : 3
-}
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/0.5": { "bioformats2raw.layout": 3 }
+  }
+}

latest/examples/bf2raw/plate.json

@@ -1,22 +1,35 @@
 {
-  "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
-    } ],
-    "version" : "0.4"
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/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
+          }
+        ]
+      }
+    }
   }
 }

latest/examples/label_strict/colors_properties.json

@@ -1,31 +1,36 @@
 {
-  "image-label": {
-    "version": "0.5-dev",
-    "colors": [
-      {
-        "label-value": 0,
-        "rgba": [0, 0, 128, 128]
-      },
-      {
-        "label-value": 1,
-        "rgba": [0, 128, 0, 128]
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/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": "../../"
+        }
       }
-    ],
-    "properties": [
-      {
-        "label-value": 0,
-        "area (pixels)": 1200,
-        "class": "intercellular space"
-      },
-      {
-        "label-value": 1,
-        "area (pixels)": 1650,
-        "class": "cell",
-        "cell type": "neuron"
-      }
-    ],
-    "source": {
-      "image": "../../"
     }
   }
 }

latest/examples/multiscales_strict/multiscales_example.json

@@ -1,54 +1,67 @@
 {
-    "multiscales": [
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/0.5": {
+      "multiscales": [
         {
-            "version": "0.5-dev",
-            "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": [
+          "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": [
                 {
-                    "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]
-                    }]
-                },
+                  // 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": [
                 {
-                    "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]
-                    }]
-                },
+                  // 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": [
                 {
-                    "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]
-                    }]
+                  // 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}
+              ]
+            }
+          ],
+          "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 }
+          }
         }
-    ]
-}
+      ]
+    }
+  }
+}

latest/examples/multiscales_strict/multiscales_transformations.json

@@ -1,47 +1,46 @@
 {
-    "multiscales": [
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/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": [
+          "axes": [
+            {
+              "name": "y",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "x",
+              "type": "space",
+              "unit": "micrometer"
+            }
+          ],
+          "datasets": [
+            {
+              "path": "0",
+              "coordinateTransformations": [
                 {
-                    "scale": [
-                        10,
-                        10
-                    ],
-                    "type": "scale"
+                  "scale": [1, 1],
+                  "type": "scale"
                 }
-            ],
-            "version": "0.5-dev",
-            "name": "image_with_coordinateTransformations",
-            "type": "foo",
-            "metadata": {
-                "key": "value"
+              ]
+            }
+          ],
+          "coordinateTransformations": [
+            {
+              "scale": [10, 10],
+              "type": "scale"
             }
+          ],
+          "name": "image_with_coordinateTransformations",
+          "type": "foo",
+          "metadata": {
+            "key": "value"
+          }
         }
-    ]
-}
+      ]
+    }
+  }
+}

latest/examples/ome/series-2.json

@@ -1,3 +1,9 @@
 {
-  "series" : [ "0", "1" ]
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "https://ngff.openmicroscopy.org/0.5": {
+      "series": ["0", "1"]
+    }
+  }
 }