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Merge pull request #267 from KPMP/develop
Atlas 2024 Q3 Release
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179 changes: 179 additions & 0 deletions
179
src/components/SpatialViewer/segmentationViewConfig.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,179 @@ | ||
| { | ||
| "version": "1.0.16", | ||
| "name": "KPMP Spatial Viewer", | ||
| "description": "Segmentation Masks & Pathomics Vectors", | ||
| "datasets": [ | ||
| { | ||
| "uid": "A", | ||
| "name": "My dataset", | ||
| "files": [ | ||
| { | ||
| "name": "<SEGMENTATION_MASK_NAME>", | ||
| "url": "<SEGMENTATION_MASK_URL>", | ||
| "fileType": "obsSegmentations.ome-tiff", | ||
| "options": { | ||
| "obsTypesFromChannelNames": true, | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "scale", | ||
| "scale": [ | ||
| "<PHYSICAL_SIZE_X>", | ||
| "<PHYSICAL_SIZE_Y>", | ||
| 1, | ||
| 1, | ||
| 1 | ||
| ] | ||
| } | ||
| ] | ||
| }, | ||
| "coordinationValues": { | ||
| "fileUid": "<SEGMENTATION_MASK_NAME>" | ||
| } | ||
| }, | ||
| { | ||
| "name": "<IMAGE_NAME>", | ||
| "url": "<IMAGE_URL>", | ||
| "fileType": "image.ome-tiff", | ||
| "coordinationValues": { | ||
| "fileUid": "<IMAGE_NAME>" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinationSpace": { | ||
| "dataset": { | ||
| "A": "A" | ||
| }, | ||
| "spatialChannelOpacity": "<SPATIAL_CHANNEL_OPACITY>", | ||
| "imageLayer": { | ||
| "A": "<IMAGE_NAME>" | ||
| }, | ||
| "fileUid": { | ||
| "A": "<IMAGE_NAME>", | ||
| "B": "<SEGMENTATION_MASK_NAME>" | ||
| }, | ||
| "photometricInterpretation": { | ||
| "A": "RGB" | ||
| }, | ||
| "spatialTargetC": "<SPATIAL_TARGET_C>", | ||
| "spatialChannelColor": "<SPATIAL_CHANNEL_COLOR>", | ||
| "spatialChannelVisible": "<SPATIAL_CHANNEL_VISIBLE>", | ||
| "spatialSegmentationFilled": "<FILLED>", | ||
| "spatialSegmentationStrokeWidth": "<STROKE_WIDTH>", | ||
| "segmentationLayer": { | ||
| "A": "Segmentation Masks" | ||
| }, | ||
| "segmentationChannel": "<SEGMENTATION_CHANNEL>", | ||
| "obsType": "<OBS_TYPE>", | ||
| "obsColorEncoding": "<OBS_COLOR_ENCODING>", | ||
| "metaCoordinationScopes": { | ||
| "A": { | ||
| "spatialZoom": "A", | ||
| "imageLayer": [ | ||
| "A" | ||
| ], | ||
| "segmentationLayer": [ | ||
| "A" | ||
| ] | ||
| } | ||
| }, | ||
| "metaCoordinationScopesBy": { | ||
| "A": { | ||
| "imageLayer": { | ||
| "fileUid": { | ||
| "A": "A" | ||
| }, | ||
| "photometricInterpretation": { | ||
| "A": "A" | ||
| }, | ||
| "imageChannel": { | ||
| "A": [ | ||
| "A", | ||
| "B", | ||
| "C" | ||
| ] | ||
| } | ||
| }, | ||
| "imageChannel": { | ||
| "spatialTargetC": { | ||
| "A": "A", | ||
| "B": "B", | ||
| "C": "C" | ||
| }, | ||
| "spatialChannelColor": { | ||
| "A": "A", | ||
| "B": "B", | ||
| "C": "C" | ||
| }, | ||
| "spatialChannelVisible": { | ||
| "A": "A", | ||
| "B": "B", | ||
| "C": "C" | ||
| }, | ||
| "spatialChannelOpacity": { | ||
| "A": "A", | ||
| "B": "B", | ||
| "C": "C" | ||
| }, | ||
| "spatialChannelWindow": { | ||
| "A": "A", | ||
| "B": "B", | ||
| "C": "C" | ||
| } | ||
| }, | ||
| "segmentationLayer": { | ||
| "fileUid": { | ||
| "A": "B" | ||
| }, | ||
| "segmentationChannel": "<COORD_SEGMENTATION_CHANNEL>" | ||
| }, | ||
| "segmentationChannel": { | ||
| "obsType": "<COORD_OBS_TYPE>", | ||
| "spatialTargetC": "<COORD_SPATIAL_TARGET_C>", | ||
| "spatialChannelColor": "<COORD_SPATIAL_CHANNEL_COLOR>", | ||
| "spatialChannelOpacity": "<COORD_SPATIAL_CHANNEL_OPACITY>", | ||
| "spatialChannelVisible": "<COORD_SPATIAL_CHANNEL_VISIBLE>", | ||
| "spatialSegmentationFilled": "<COORD_FILLED>", | ||
| "spatialSegmentationStrokeWidth": "<COORD_STROKE_WIDTH>", | ||
| "obsColorEncoding": "<COORD_OBS_COLOR_ENCODING>" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "layout": [ | ||
| { | ||
| "component": "spatialBeta", | ||
| "coordinationScopes": { | ||
| "dataset": "A", | ||
| "metaCoordinationScopes": [ | ||
| "A" | ||
| ], | ||
| "metaCoordinationScopesBy": [ | ||
| "A" | ||
| ] | ||
| }, | ||
| "x": 0, | ||
| "y": 0, | ||
| "w": 6, | ||
| "h": 12 | ||
| }, | ||
| { | ||
| "component": "layerControllerBeta", | ||
| "coordinationScopes": { | ||
| "dataset": "A", | ||
| "metaCoordinationScopes": [ | ||
| "A" | ||
| ], | ||
| "metaCoordinationScopesBy": [ | ||
| "A" | ||
| ] | ||
| }, | ||
| "x": 6, | ||
| "y": 0, | ||
| "w": 6, | ||
| "h": 12 | ||
| } | ||
| ], | ||
| "initStrategy": "auto" | ||
| } |
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