igneous
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Why is the browser stuck when visualizing the generated surface mesh?
I have been trying to visualize a large volume, with 2000x2000x1000 voxels. I created a configuration file using CloudVolume.create_new_info
, which I set the chunk to be 100x100x50 voxels. And then I use the following code to create downsampled data and visualizing in neuroglancer. However, when I tried to visualize the mesh in the neuroglancer, it become very laggy, which is almost impossible to interact with. I am wondering if there were ways to make it faster for visulization? I tried downsample the image with --mip-level 4
added, but still it was not helping.
igneous image downsample file://./ --mip 0 --queue ./ds-queue
igneous --parallel 20 execute -x ./ds-queue
igneous mesh forge file://./ --mip 0 --queue ./mesh-queue
igneous --parallel 20 execute -x ./mesh-queue
igneous mesh merge file://./ --queue ./mesh-queue
igneous --parallel 20 execute -x ./mesh-queue
igneous view ./ --port 6220
I think i see what the problem is. Try meshing from a higher mip level, that will radically simplify the meshes.
Usually I try to pick a near isotropic mip level.
On Fri, Oct 6, 2023, 1:02 PM HHHIT @.***> wrote:
I have been trying to visualize a large volume, with 2000x2000x1000 voxels. I created a configuration file using CloudVolume.create_new_info, which I set the chunk to be 100x100x50 voxels. And then I use the following code to create downsampled data and visualizing in neuroglancer. However, when I tried to visualize the mesh in the neuroglancer, it become very laggy, which is almost impossible to interact with. I am wondering if there were ways to make it faster for visulization? I tried downsample the image with --mip-level 4 added, but still it was not helping.
igneous image downsample file://./ --mip 0 --queue ./ds-queue igneous --parallel 20 execute -x ./ds-queue igneous mesh forge file://./ --mip 0 --queue ./mesh-queue igneous --parallel 20 execute -x ./mesh-queue igneous mesh merge file://./ --queue ./mesh-queue igneous --parallel 20 execute -x ./mesh-queue igneous view ./ --port 6220
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Thank you. Now, with the mip-level 4 as the input for generating the mesh, I can visualize in the browser more smoothly. However, the quality is really bad due to the low resolution. I am wondering if I can generate more levels of mesh? so that when I zoom in, the finer details of the mesh will be displayed.
Yes, you can do that by generating the sharded multi-resolution meshes.
Is the parameter nlod used to decide how many levels of mesh to generate?
Yes, it sets the max number to generate though not the precise number.
On Sun, Oct 8, 2023, 5:42 PM HHHIT @.***> wrote:
Is the parameter nlod used to decide how many levels of mesh to generate?
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Thanks a lot! I have tried using the shared format, but I still found it only displays the mesh with only one resolution. Are there any issues in my following command? Thanks,
igneous image downsample file://./ --mip 0 --num-mips 4 --queue ./ds-queue
igneous --parallel 20 execute -x ./ds-queue/
igneous mesh forge file://./ --mip 4 --queue ./mesh-queue --sharded
igneous --parallel 20 execute -x ./mesh-queue
igneous mesh merge-sharded file://./ --queue ./mesh-queue --nlod 4
igneous --parallel 20 execute -x ./mesh-queue
igneous view ./ --port 6220
I think you'll want to forge from a lower mip level for meshing if you want the multi-res stuff to be usable. The mip level sets the floor on the resolution you can obtain.