RFC-8: Collections

rfc/8/examples/README.md

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+# RFC-8 Examples
+
+* `webknossos/custom-nodes.json`: A typical Webknossos collection with EM data, affinity prediction and segmentation as well as some custom nodes for meshes, segment index, agglomeration and connectome.
+* `webknossos/inline-multiscale.json`: Same as `webknossos/custom-nodes.json` but with inlined multiscale metadata (non-standard, just as an experiment).

rfc/8/examples/webknossos/custom-nodes.json

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+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.7",
+      "type": "collection",
+      "name": "l4dense_motta_et_al_dev_v2",
+      "attributes": {
+        "webknossos:rendering": {
+          "position": { "x": 2850, "y": 4318, "z": 1770 },
+          "zoom": 1.3,
+          "voxel_size": {
+            "factor": [11.239999771118164, 11.239999771118164, 28],
+            "unit": "nanometer"
+          }
+        }
+      },
+      "nodes": [
+        {
+          "type": "multiscale",
+          "name": "color",
+          "attributes": {
+            "webknossos:category": "color",
+            "webknossos:bounding_box": {
+              "topleft": { "x": 128, "y": 128, "z": 128 },
+              "size": { "x": 5445, "y": 8380, "z": 3285 }
+            },
+            "webknossos:data_type": "uint8"
+          },
+          "path": "/absolute/path/to/l4dense_motta_et_al_demo/color"
+        },
+        {
+          "type": "multiscale",
+          "name": "segmentation",
+          "attributes": {
+            "webknossos:category": "segmentation",
+            "webknossos:bounding_box": {
+              "topleft": { "x": 0, "y": 0, "z": 0 },
+              "size": { "x": 5632, "y": 8704, "z": 3584 }
+            },
+            "webknossos:data_type": "uint32",
+            "webknossos:values": { "max": 100000 }
+          },
+          "path": "./segmentation"
+        },
+        {
+          "type": "webknossos:mesh",
+          "name": "meshfile_4-4-2",
+          "path": "./segmentation/zarr/meshes/meshfile_4-4-2",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_5",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_5",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_10",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_10",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_15",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_15",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_20",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_20",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_25",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_25",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_30",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_30",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_35",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_35",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_40",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_40",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_45",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_45",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_50",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_50",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_55",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_55",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_60",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_60",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_65",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_65",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_70",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_70",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_75",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_75",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_80",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_80",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_85",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_85",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_90",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_90",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_95",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_95",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:agglomeration",
+          "name": "agglomerate_view_100",
+          "path": "./segmentation/zarr/agglomerates/agglomerate_view_100",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:segment_index",
+          "name": "segmentIndex",
+          "path": "./segmentation/zarr/segmentIndex/segmentIndex",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "webknossos:connectome",
+          "name": "paper_l4_full_connectome",
+          "path": "./segmentation/zarr/connectomes/paper_l4_full_connectome",
+          "attributes": { "webknossos:parent": "segmentation" }
+        },
+        {
+          "type": "multiscale",
+          "name": "prediction",
+          "attributes": {
+            "webknossos:category": "color",
+            "webknossos:bounding_box": {
+              "topleft": { "c": 0, "x": 128, "y": 128, "z": 128 },
+              "size": { "c": 3, "x": 5445, "y": 8380, "z": 3285 }
+            },
+            "webknossos:data_type": "uint8",
+            "webknossos:rendering": { "is_disabled": true }
+          },
+          "path": "./prediction"
+        }
+      ]
+    }
+  }
+}