Neuroglancer link generation

[stuarteberg]

It should be relatively easy to write a convenience function to programmatically generate neuroglancer links showing selected bodies, ROIs, and perhaps synapses.

Here's an example neuroglancer link.

And here's a script that parses neuroglancer links into human-readable form.

And here's what the human-readable version of the above link looks like.

https://hemibrain-dot-neuroglancer-demo.appspot.com/#!    
{
    "dimensions": {
        "x": [
            8e-09,
            "m"
        ],
        "y": [
            8e-09,
            "m"
        ],
        "z": [
            8e-09,
            "m"
        ]
    },
    "position": [
        25055.619140625,
        20692.138671875,
        15192.470703125
    ],
    "crossSectionScale": 66.24585188318474,
    "crossSectionDepth": -37.62185354999912,
    "projectionOrientation": [
        -0.21849310398101807,
        0.07027091830968857,
        0.08402863889932632,
        0.9696710705757141
    ],
    "projectionScale": 39285.54718181589,
    "layers": [
        {
            "type": "image",
            "source": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/emdata/clahe_yz/jpeg",
            "name": "emdata"
        },
        {
            "type": "segmentation",
            "source": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation",
            "segments": [
                "910442723",
                "915273354"
            ],
            "name": "segmentation"
        },
        {
            "type": "segmentation",
            "source": {
                "url": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/rois",
                "subsources": {
                    "default": true,
                    "properties": true,
                    "mesh": true
                },
                "enableDefaultSubsources": false
            },
            "pick": false,
            "saturation": 0.59,
            "objectAlpha": 0.8,
            "ignoreNullVisibleSet": false,
            "colorSeed": 2685294016,
            "meshSilhouetteRendering": 3,
            "segments": [
                "20",
                "36"
            ],
            "name": "roi"
        },
        {
            "type": "annotation",
            "source": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/v1.0/synapses",
            "tab": "rendering",
            "shader": "#uicontrol vec3 preColor color(default=\"red\")\n#uicontrol vec3 postColor color(default=\"blue\")\n#uicontrol float preConfidence slider(min=0_ max=1_ default=0)\n#uicontrol float postConfidence slider(min=0_ max=1_ default=0)\n\nvoid main() {\n  setColor(defaultColor());\n  setEndpointMarkerColor(\n    vec4(preColor_ 0.5)_\n    vec4(postColor_ 0.5));\n  setEndpointMarkerSize(2.0_ 2.0);\n  setLineWidth(2.0);\n  if (prop_pre_synaptic_confidence()< preConfidence ||\n      prop_post_synaptic_confidence()< postConfidence) discard;\n}\n",
            "ignoreNullSegmentFilter": false,
            "linkedSegmentationLayer": {
                "pre_synaptic_cell": "segmentation",
                "post_synaptic_cell": "segmentation"
            },
            "filterBySegmentation": [
                "post,synaptic,cell",
                "pre,synaptic,cell"
            ],
            "name": "synapse",
            "visible": false
        },
        {
            "type": "segmentation",
            "source": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/mito_20190717.27250582",
            "tab": "segments",
            "pick": false,
            "selectedAlpha": 0.82,
            "name": "mito",
            "visible": false
        },
        {
            "type": "segmentation",
            "source": "precomputed://gs://neuroglancer-janelia-flyem-hemibrain/mask_normalized_round6",
            "tab": "segments",
            "pick": false,
            "selectedAlpha": 0.53,
            "segments": [
                "2"
            ],
            "name": "mask",
            "visible": false
        }
    ],
    "showSlices": false,
    "selectedLayer": {
        "layer": "roi",
        "visible": true,
        "size": 290
    },
    "layout": "4panel",
    "selection": null
}