HenriquesLab / HenriquesLab/VLab4Mic

Modality pixelsize_nm must be divisible by psf_voxel_nm

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Python
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Description

Describe the bug
When changing modality parameters in vLab4Mic main notebook using myexperiment.update_modality(), the pixel size must be a value that is divisible by the psf voxel size, otherwise the acquisition preview does not load. Changing the psf voxel size to 1 does overcome this, but it takes too long to load even the acquisition preview to test this for full simulation.

To Reproduce
Steps to reproduce the behavior:

  1. Run Jupyter notebook vLab4Mic-main
  2. Load in structrue (e.g. 7R5K)
  3. Load in probe (e.g. NPC_Nup96_Cterminal_direct with defaults)
  4. Load in virtual sample paramters (e.g. 1 particle with no randomisation)
  5. Edit confocal modality using line:
    my_experiment.update_modality("Confocal", 45, 170,340)
  6. select confocal modality and update virtual microscope (toggle psf view should show: pixel size at 45 nm; lateral res at 170 nm; axial res at 340 nm; and depth of field at 1000 nm)
  7. Select acquisition parameters: confocal; select all chanels
  8. update acquisition parameters and select interactive acquisiont preview
  9. See error:
    nothing shows up for the acquisition preview in this case.

Expected behavior
Expect to see a preview of the virtual sample with edited acquisition parameters at this stage.

Desktop (please complete the following information):

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

Additional context
If you change the confocal modality voxel size parameter to a multiple of the pixel size, e.g. 15, replacing the code in step 5 with my_experiment.update_modality("Confocal", 45, 170,340,15), then a virtual sample preview will appear at step 9.

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in the vLab4Mic-main notebook and reproduce the issue with update_modality("Confocal", 45, 170, 340), then compare it with the voxel-size-15 example. Trace the interactive acquisition preview path after selecting all channels; done when the reported modality parameters produce a working preview or the incompatibility is explicitly handled.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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