HenriquesLab / HenriquesLab/VLab4Mic
Modality pixelsize_nm must be divisible by psf_voxel_nm
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- Dominant language
- Python
- Stars
- 3
- Forks
- 0
- PR merge metrics
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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:
- Run Jupyter notebook vLab4Mic-main
- Load in structrue (e.g. 7R5K)
- Load in probe (e.g. NPC_Nup96_Cterminal_direct with defaults)
- Load in virtual sample paramters (e.g. 1 particle with no randomisation)
- Edit confocal modality using line:
my_experiment.update_modality("Confocal", 45, 170,340) - 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)
- Select acquisition parameters: confocal; select all chanels
- update acquisition parameters and select interactive acquisiont preview
- 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.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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