Xeniumranger import-segmentation producing different cell polygons (less than 4 vertices polygons)

[ConstensouxAlexis]

Hello,
I ran Baysor v0.7, and tried to import the segmentation results with xeniumranger 3.1 import-segmentation. I followed the steps explained in 10x website, and made sure the files format (geojson GeometryCollection) was correct. Each cell in the polygons.geojson have more than 4 vertices.
However, few cells have a different polygon shape after running xeniumranger import segmentation. Some cells end up having less than 4 vertices, which cause the python reader of the package I am using (spatialdata) to fail, because polygons needs to have at least 4 vertices. I am wondering if you know what could be the origin of this, maybe an issue the polygons.geojson file or in the segmentation.csv ?

Thank you very much !

[LoganAMorrison]

@ConstensouxAlexis 10x xeniumranger dev here:

That is very curious. Is it possible for you to provide one of the problematic polygons? (e.g., one that had more than 4 vertices and which had less than 4 vertices in the outputs.)

One scenario that comes to mind where this could happen is if the polygon is actually 2D. For example, something like:

{
  "geometries":[
    {
       "coordinates":[
         [
           [1.0, 1.0],
           [2.0, 2.0],
           [1.0, 1.0],
           [1.0, 1.0]
         ]
       ],
       "type":"Polygon",
       "cell":1
    },
    {
       "coordinates":[
         [
           [1.0, 1.0],
           [2.0, 2.0],
           [3.0, 3.0],
           [1.0, 1.0]
         ]
       ],
       "type":"Polygon",
       "cell":2
    }
  ],
  "type":"GeometryCollection"
}