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