MM Ome tif support

[amitabhverma]

• Added CLI support for Micro-Manager acquired ome tif datasets: converts to .zarr and then proceeds to reconstruction.
• Added GUI functionality to support ome-tif
• Added metadata info next to dataset selector utilizing "iohub info" like functionality

Incorporated changes based on comments from previous pull request #527

[codecov]

Codecov Report

❌ Patch coverage is 27.94118% with 98 lines in your changes missing coverage. Please review.
✅ Project coverage is 52.45%. Comparing base (507a8af) to head (13e4d01).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
waveorder/cli/utils.py	29.87%	54 Missing ⚠️
waveorder/plugin/tab_recon.py	15.38%	33 Missing ⚠️
waveorder/cli/apply_inverse_transfer_function.py	50.00%	3 Missing ⚠️
waveorder/cli/compute_transfer_function.py	40.00%	3 Missing ⚠️
waveorder/cli/reconstruct.py	40.00%	3 Missing ⚠️
waveorder/cli/parsing.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #564      +/-   ##
==========================================
- Coverage   55.49%   52.45%   -3.05%     
==========================================
  Files          62       62              
  Lines       11051    11654     +603     
==========================================
- Hits         6133     6113      -20     
- Misses       4918     5541     +623     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[talonchandler]

Hi @amitabhverma, thanks for this iteration.

The main shape of this feature is correct, but much of what's here duplicates code that lives in iohub. I just pushed a feature/ometiff-input branch that refactors to show what a minimal version would look like. By reusing iohub and moving the switching in parsing.py, we reduce the feature diff to <50 lines.

Regarding pinned dependencies, let's figure this out with automated tests. In my example branch I added a test that checks a simple ome.tiff against the current pyproject.toml, and I couldn't reproduce the issues you mentioned. If you saw failures, can you share:

• the traceback,
• the iohub, tifffile, zarr versions in the failing environment,
• the path/dataset that triggered the issue, and
• ideally, a failing automated test that reproduces the problem.

If we need to pin versions, this PR should include a change to pyproject.toml and an automated test that fails without the pin.

[talonchandler]

Final fixes made together. Looks great! Thanks @amitabhverma

[amitabhverma]

@talonchandler

Couple of points I forgot to ask/share on Friday.

1. For ome-zarr metadata print_info does not print out the Scale and FOV which are the 2 additions I had to do on my end. Do you use something else to get that info using iohub ? Ideally, like we discussed, this function should reside in iohub with a wrapper on waveorder.

2. I moved some other metadata parsing which was under tab_recon to utils.get_dataset_info which adds those extra fields and also provides easier access to fields that might be needed for auto-populate. Regarding auto-populate, is it explicit that there would only be a single channel when doing a Phase/Fluorescence reconstruction ?

3. I was trying the pytest and trying to locate what you had shown me and realized the version on https://waveorder.readthedocs.io/en/latest/guide/development-guide.html is different from whats in the /main branch docs are. I believe I had it set to automatically generate the html docs with a new commit but it seems like it's not done that for the last 10 months.

4. I got the tests running locally now but had to manually install pytest-qt

[talonchandler]

Thanks Amit...following up with a summary of our chat just now:

1. I'm flexible on this...you can leave it as is and/or pass in single FOVs in the print_info.

2. Yes, only a single channel for fluorescence and phase. Birefringence recons can take multiple input channels.

3. No worries. Github docs is fine for now...Sri will likely move + rebuild our docs later.

4. We worked through this together...see CONTRIBUTING.md. Feel free to flag/fix conflicting instructions.