Error showing when showing virtual sample after selecting sample parameters

[tshakespeare]

Describe the bug
Error appears in Jupyter labs, seemingly related to

To Reproduce
Steps to reproduce the behavior:

1. Load in structure in vLab4Mic notebook (7R5K)
2. Set parameters for visualisation:

• 10 particles; random orientation; random focal depth; min distance between particles = 100 nm; pixel size 100 nm (shown in screenshot)

3. update sample parameters
4. Select paramters and build virtual sample
5. Show virtual sample
6. See error:
   /Users/taylashakespeare/miniconda3/envs/vlab-test/lib/python3.11/site-packages/mpl_toolkits/mplot3d/art3d.py:1403: RuntimeWarning: divide by zero encountered in matmul
   shade = ((normals / np.linalg.norm(normals, axis=1, keepdims=True))
   /Users/taylashakespeare/miniconda3/envs/vlab-test/lib/python3.11/site-packages/mpl_toolkits/mplot3d/art3d.py:1403: RuntimeWarning: overflow encountered in matmul
   shade = ((normals / np.linalg.norm(normals, axis=1, keepdims=True))

Virtual sample loads (screenshot 2) and error doesn´t seem to impact workflow from here. However, axes seem ´crowded´

Expected behavior

Don´t expect to get error and plot axes should be cramped/ overlapping

Screenshots

Desktop (please complete the following information):

• OS: iOS
• Browser: Firefox
• Version: 145.0.2

Additional context
When run it again by updating parameters and shwoing virtual sample, still have crowded plot axes, but error goes away