README.md

Sekleton Server

This is a small web service to serve CATMAID skeletons as a neuroglancer datasource.

Usage

Run the server, e.g. flask run after installing dependencies.

Neuroglancer layer definition

For FAFBv14, no translation:

{
    "type": "segmentation",
    "name": "VFB Skeletons",
    "source": "precomputed://http://127.0.0.1:5000/catmaid/vfb_fafb/skeleton/",
    "segments": [
        "815776"
    ],
    "selectedAlpha": 0,
        "skeletonRendering": {
        "mode2d": "lines",
        "lineWidth2d": 25,
        "mode3d": "lines_and_points",
        "lineWidth3d": 10
    }
}

For FAFBv14, with translation to FlyWire:

{
    "type": "segmentation",
    "name": "VFB Skeletons",
    "source": "precomputed://http://127.0.0.1:5000/catmaid/vfb_fafb/transform/v14_to_flywire/skeleton/",
    "segments": [
        "815776"
    ],
    "selectedAlpha": 0,
        "skeletonRendering": {
        "mode2d": "lines",
        "lineWidth2d": 25,
        "mode3d": "lines_and_points",
        "lineWidth3d": 10
    }
}

Notes

• Dimensions are currently using the FAFB extents

References

• neuroglancer skeleton spec