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seung-lab / zmesh

Marching Cubes & Mesh Simplification on multi-label 3D images.
GNU General Public License v3.0
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Neuroglancer precomputed format #18

Closed Mencu closed 3 years ago

Mencu commented 3 years ago

Hello,

how should one use that precomputed mesh for Neuroglancer? When starting Neuroglancer up, it throws an error:

"Error retrieving chunk 13955040: Error: Error parsing "fragments" property: Expected array, received: ".../meshes/13955040"."

'meshes' is the directory of the mesh data and we are trying to get the mesh of id 13955040.

As per Neuroglancer documentation, the ":0" should be a JSON metadata file, and not the mesh bytes file. Did zmesh bypass this in any way?

Any response is much appreciated.

Best regards, Andrei Mancu

william-silversmith commented 3 years ago

Hi Andrei,

While zmesh can produce precomputed mesh binaries, it really doesn't know very much about Neuroglancer, it's purely designed for meshing.

I would recommend checking out https://github.com/seung-lab/igneous which is designed for producing Neuroglancer compatible mesh files.

The Neuroglancer manifest file should contain the JSON { "fragments": [ "13955040:0:some_bounding_box", ... ] }

The files referenced in the manifest should be precomputed binary mesh files.

william-silversmith commented 3 years ago

Closing due to inactivity. Please reopen if you still need help!