Closed sommerc closed 4 years ago
In the source tab of the segmentation channel appears the error msg:
Error parsing "sharding" property: Expected JSON object, but received: null.
I tried to set it to false
but then another JSON error pops up...
Hi Sommerc! Thanks for pointing out that problem in the documentation. How are you using Neuroglancer? Another person was using a locally hosted version and had some problems viewing meshes. Have you tried using https://neuroglancer-demo.appspot.com ?
Some older versions of Neuroglancer don't like info files in the skeleton directory when the data are not sharded. You can try deleting the info file there and using https://neuromancer-seung-import.appspot.com/ which we have modified to work with that.
Thanks for the fast reply!
I am running neuroglancer locally from a very recent checkout. Also my precomputed volumes, I serve locally with the cors_webserver shipped with neuroglancer.
I tried https://neuroglancer-demo.appspot.com with the same error msg Error parsing "sharding" property: Expected JSON object, but received: null
After removing the property sharding
from the info file completely, I get Data type not supported by WebGL: UINT8
On https://neuromancer-seung-import.appspot.com/, I can actually load the segmentation layer again, meshes are displayed but the skeletons not. There's an error in the Skeleton shader: 'assign' cannot convert from 'structure' to 'out highp float'
Ah, I am familiar with (at least part of) this problem. I'm not sure what that last error with neuromancer-seung-import.appspot.com is, but the UINT8 issue is that the neuroglancer shaders do not support reading the optional vertex_types attribute that get attached the the skeletons. I think it would prefer float or double types. Many people do nothing with those attributes, so they are all set to zero.
I'll modify the skeletonizing tasks to include a parameter that switches off the vertex_types and that will probably fix it if you rerun it.
Great, thanks a lot!
Okay! There's a new version on master that should do what you need.
I tried to create skeltons with the new master, however, I got an error in merge task related with vertex attributes:
sorry, my bad, forgot to delete old folder
The skeletons are now recognized in my local neuroglancer instance... unfortunately, they are not displayed.
I see this error in the skelton shader:
That sounds like an ANGLE-related issue converting the GLSL code to HLSL... (ANGLE is activated by default in browsers on Windows) You could try to enforce using the native OpenGL drivers: https://github.com/mrdoob/three.js/wiki/How-to-use-OpenGL-or-ANGLE-rendering-on-Windows
Just tried with chrome.exe --use-angle=gl
, unfortunately same error
Hm, if it is still showing "Failed to create D3D Shaders", ANGLE still seems to be active. You can verify that here: https://browserleaks.com/webgl - look for a row that says ANGLE
. Did you close all Chrome instances before restarting with --use-angle=gl
?
Are the files decompressed? Maybe your web server isn't handling compression correctly.
Are the files decompressed? Maybe your web server isn't handling compression correctly. Bingo!
Thanks a lot for your help, would have never managed without.
Is there a local webserver you recommend, which handles transparent gz? The cors_webserver.py from neuroglancer obviously doesn't?
If your needs are very simple, you can use the one embedded in CloudVolume.
cv = CloudVolume(...)
cv.viewer()
Hi all,
thanks for this cool library.
I am generating skeltons from a local precomputed segmentation layer. And it worked after changing the function name to
create_skeletonizing_tasks()
. (the doc sayscreate_skeletonization_tasks()
)However, in neuroglancer, the skeletons are not recognized / displayed. The info file points to the correct skeletons folder.
Any pointers what I am doing wrong?
Cheers, Chris