Questions on loading mesh obj files about neuroglancer HOT 6 OPEN

Most likely the issue with the precomputed mesh is just as you say, that it is rendered somewhere far away. Unfortunately at the moment Neuroglancer does not provide much help with "finding it" for the single-resolution meshes. For multi-resolution meshes there is additional bounding box information available.

For precomputed meshes, the coordinates are supposed to be in nanometers. If they are instead in voxels, you will need to apply a transform in Neuroglancer.

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There is currently no collection of .obj files data source, but you could add one easily enough.

I think you could use https://github.com/seung-lab/cloud-volume to convert from obj to neuroglancer precomputed mesh format.

Opacity can be changed via a shader UI control. For silhouette rendering, it is technically possible at the moment but relies on certain implementation details that are exposed to the shader:

float absCosAngle = vLightingFactor - uLightDirection.w;
float silhouetteFactor = pow(1.0 - absCosAngle, silhouette_power);
emitPremultipliedRGBA(color * silhouetteFactor);

But that is not guaranteed to work in the future. It would be better instead to modify neuroglancer to explicitly expose the normal to the shader.

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The color must be vec3 as noted in the error. The alpha value you can supply through a separate opacity control. getDataValue() is only available in image layers there is no specific "data value". Instead you should use emitPremultipliedRGBA(vec4(color, opacity));

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Hello, @jbms

Thank you for the guidance here.

I think you could use https://github.com/seung-lab/cloud-volume to convert from obj to neuroglancer precomputed mesh format.

Yes, I'm also trying this approach and for whatever the reason the mesh does not load up. Obviously, I don't have an image layer but the precomputed mesh seemed to have loaded. Chunk statics shows otherwise so I'm guessing it may be rendered far away from the view??? I'm doubting if info file under the mesh folder is misconfigured. Thoughts?

(info)

{
  "data_type": "uint32",
  "mesh": "mesh",
  "num_channels": 1,
  "scales": [
    {
      "chunk_sizes": [
        [
          64,
          64,
          64
        ]
      ],
      "encoding": "raw",
      "key": "50000_50000_50000",
      "resolution": [
        50000,
        50000,
        50000
      ],
      "size": [
        228,
        160,
        264
      ],
      "voxel_offset": [
        0,
        0,
        0
      ]
    }
  ],
  "type": "segmentation"

(mesh/info)

{"@type":"neuroglancer_legacy_mesh","mip":0,"chunk_size":[128,128,128],"spatial_index":{"resolution":[50000,50000,50000],"chunk_size":[128,128,128]}}

Opacity can be changed via a shader UI control.

That is good to know! However, I'm getting these Shader errors in the Shader console. Attached screenshots. Do I need to update Neuroglancer version?

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This worked. Thank you @jbms !! Regarding the visualization of precomputed mesh, how should I approach to debug the issue? I can't seem to identify how to catch what's preventing from loading a precomputed mesh on the Neuroglancer viewer. Chrome Dev Tool hasn't given much clue except "getHtmlPathCompletions" in the console, and 404 for chunks requested on images which are not available. Any thoughts here?

#uicontrol vec3 color color(default="gray")
#uicontrol float opacity slider(default=0.5, min=0, max=1, step=0.1)
#uicontrol float silhouette_power slider(default=0.5, min=0, max=1, step=0.1)
  
void main() {
  float absCosAngle = vLightingFactor - uLightDirection.w;
  float silhouetteFactor = pow(1.0 - absCosAngle, silhouette_power);

  emitPremultipliedRGBA(vec4(color * silhouetteFactor, opacity));
}

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As you mentioned, after playing around with the transformation matrix, and setting to 1 with additional scaling, the mesh appeared as expected! Thank you for the help here.

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