vitessce-python/demos/wang-2018/vitessce.template.json at 3e64faee7cf10965548b87450cbee0ced405f3f9 · vitessce/vitessce-python · GitHub

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{
  "name": "Wang et al., Scientific Reports 2018",
  "version": "1.0.15",
  "description": "Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy",
  "public": true,
  "datasets": [
    {
      "uid": "wang-2018",
      "name": "Wang 2018",
      "files": [
        {
          "fileType": "obsSegmentations.json",
          "url": "{{ base_url }}/wang_2018_scientific_reports.cells.segmentations.json",
          "coordinationValues": {
            "obsType": "cell"
          }
        },
        {
          "fileType": "obsLocations.csv",
          "url": "{{ base_url }}/wang_2018_scientific_reports.cells.csv",
          "options": {
            "obsIndex": "cell_id",
            "obsLocations": ["X", "Y"]
          },
          "coordinationValues": {
            "obsType": "cell"
          }
        },
        {
          "fileType": "obsLocations.csv",
          "url": "{{ base_url }}/wang_2018_scientific_reports.molecules.csv",
          "options": {
            "obsIndex": "molecule_id",
            "obsLocations": ["X", "Y"]
          },
          "coordinationValues": {
            "obsType": "molecule"
          }
        },
        {
          "fileType": "obsLabels.csv",
          "url": "{{ base_url }}/wang_2018_scientific_reports.molecules.csv",
          "options": {
            "obsIndex": "molecule_id",
            "obsLabels": "Gene"
          },
          "coordinationValues": {
            "obsType": "molecule"
          }
        },
        {
          "fileType": "obsFeatureMatrix.csv",
          "url": "{{ base_url }}/wang_2018_scientific_reports.cells.matrix.csv",
          "coordinationValues": {
            "obsType": "cell",
            "featureType": "gene",
            "featureValueType": "expression"
          }
        }
      ]
    }
  ],
  "initStrategy": "auto",
  "coordinationSpace": {
    "spatialZoom": {
      "A": -1
    },
    "spatialSegmentationLayer": {
      "A": {
        "opacity": 1, "radius": 0, "visible": true, "stroked": false
      }
    },
    "spatialPointLayer": {
      "A": {
        "opacity": 1, "radius": 2, "visible": true
      }
    }
  },
  "layout": [
    {
      "component": "spatial",
      "coordinationScopes": {
        "spatialZoom": "A",
        "spatialSegmentationLayer": "A",
        "spatialPointLayer": "A"
      },
      "x": 0,
      "y": 0,
      "w": 10,
      "h": 2
    },
    {
      "component": "featureList",
      "x": 10,
      "y": 0,
      "w": 2,
      "h": 2
    }
  ]
}