napari_microsam

[laraPPr]

• link to support ticket: #2024032760000841
• website: https://computational-cell-analytics.github.io/micro-sam/micro_sam.html
• installation docs: https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#from-source
• toolchain: foss/2023a
• easyblock to use: PythonBundle
• required dependencies:
  • napari
• optional dependencies:
  • ...
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (link?) / no
  • container image: yes (link?) / no
  • pre-built binaries (RHEL8 Linux x86_64): yes (link?) / no
  • easyconfig outside EasyBuild: yes / no

[boegel]

see also discussion in computational-cell-analytics/micro-sam#601

[pavelToman]

• {vis}[foss/2023a] micro-sam v1.0.1, torch_em v0.7.1, affogato v0.3.3, ... easybuilders/easybuild-easyconfigs#20636

[boegel]

to test microsam:

Also when installing the software napari microsam can you test the 3d visualization when typing the following command when importing napari: 

from napari._vispy.utils import gl
 gl.get_max_texture_sizes()
    which should return (32768, 16384)

[pavelToman]

to test microsam:

Also when installing the software napari microsam can you test the 3d visualization when typing the following command when importing napari: 

from napari._vispy.utils import gl
 gl.get_max_texture_sizes()
    which should return (32768, 16384)

I try it and got:

>>> from napari._vispy.utils import gl
>>> gl.get_max_texture_sizes()
WARNING: could not connect to display 
WARNING: Could not load the Qt platform plugin "xcb" in "" even though it was found.
WARNING: This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, webgl, xcb.

Aborted (core dumped)

When I tried it in Cluster desktop (with empanada and micro-sam plugins loaded) it returns:
(16384, 2048)
When I load only napari and try it it returns same numbers.