Minimal example for obsSegmentations.json for visualizing polygons in Spatial View about vitessce-python

[keller-mark]

Hi @J-Yash
Can you try removing the data_type parameter in the add_file?

This is a minimal example of how the config would look as JSON

{
  "name": "Codeluppi et al., Nature Methods 2018",
  "description": "Spatial organization of the somatosensory cortex revealed by osmFISH",
  "version": "1.0.15",
  "initStrategy": "auto",
  "datasets": [
    {
      "uid": "codeluppi",
      "name": "Codeluppi",
      "files": [
        {
          "fileType": "obsSegmentations.json",
          "url": "https://s3.amazonaws.com/vitessce-data/0.0.33/main/codeluppi-2018/codeluppi_2018_nature_methods.cells.segmentations.json"
        }
      ]
    }
  ],
  "coordinationSpace": {
    "spatialSegmentationLayer": {
      "A": {
        "opacity": 1,
        "radius": 0,
        "visible": true,
        "stroked": false
      }
    }
  },
  "layout": [
    {
      "component": "layerController",
      "coordinationScopes": {
        "spatialSegmentationLayer": "A"
      },
      "x": 0,
      "y": 1,
      "w": 2,
      "h": 4
    },
    {
      "component": "spatial",
      "coordinationScopes": {
        "spatialSegmentationLayer": "A"
      },
      "x": 2,
      "y": 0,
      "w": 4,
      "h": 4
    }
  ]
}

You may need to add the line

vc.link_views([spatial, lc], ["spatialSegmentationLayer"], [{ "opacity": 1, "radius": 0, "visible": True, "stroked": False }]

[J-Yash]

Awesome! That worked. Thanks for the quick response!
On a separate note, is it also possible to set the color of the polygons to a specific color?