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@aranega aranega commented Oct 31, 2025

Relates to

Description

This PR introduces the notion of InstanceSegmentationMask for the DB ingestion. We followed the recommendation and steps listed in this link.

The following screenshot and JSON fragment shows the resulting instance segmentation mask included in neuroglancer, and the related state configuration.

screen
{
	"layers": {
      "type": "segmentation",
      "source": {
        "url": "precomputed://http://localhost:9000/10442/24aug01b_Position_33_5/Reconstructions/VoxelSpacing5.006/NeuroglancerPrecompute/100-intracellular_anatomical_structure-1.0_instancesegmentationmask",
        "transform": {
          "outputDimensions": {
            "x": [
              5.006e-10,
              "m"
            ],
            "y": [
              5.006e-10,
              "m"
            ],
            "z": [
              5.006e-10,
              "m"
            ]
          },
          "inputDimensions": {
            "x": [
              5.006e-10,
              "m"
            ],
            "y": [
              5.006e-10,
              "m"
            ],
            "z": [
              5.006e-10,
              "m"
            ]
          }
        },
        "subsources": {
          "default": true,
          "mesh": true
        },
        "enableDefaultSubsources": false
      },
      "pick": false,
      "tab": "rendering",
      "selectedAlpha": 1,
      "hoverHighlight": false,
      "meshRenderScale": 2,
      "segments": [
        "1",
        "2",
        "3",
        "4",
        "5"
      ],
      "segmentColors": {
        "1": "#ff00ff",
        "2": "#800000",
        "3": "#1063ff",
        "4": "#f7bb01",
        "5": "#36fad8"
      },
      "name": "100 intracellular anatomical structure instancesegmentation"
    }
}

Note

As note/question, we unsure about the tests we introduced for the db-ingestion. We followed the same pattern than the one for annotations in general we modified:

  • foo-1.0.json for 30001/RUN1 to introduce new files;
  • conftest.py to align the file_size with the new size of foo-1.0.json;
  • test_db_annotation.py to add the injected files as part of the assertions.

The tests are passing, but we are not sure if we need to tests the db-import differently or add something else.

aranega and others added 30 commits August 15, 2025 10:52
this was causing all data to be one singular label
@kaloster
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@aranega the test coverage here looks good and comprehensive to me and follows the existing pattern 🚀

@aranega aranega marked this pull request as ready for review December 11, 2025 12:29
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3 participants