Update BrukerTiffImagingExtractor

[weiglszonja]

Update BrukerTiffImagingExtractor to handle the additional types of Bruker data (volumetric, multi color, stimulation)
WIP

[CodyCBakerPhD]

Thanks @weiglszonja

Going to enlist the help of @pauladkisson to help review this PR to get them some more experience with the workflow of managing this repository

[pauladkisson]

Changes look pretty reasonable to me. It looks like CI checks are failing due to file/path issues, could you clear that up? Or if you're using a file that isn't in the ophys testing repo, we should probably add it.

[weiglszonja]

Thanks @pauladkisson, the PR for uploading the test data is here, once it's merged hopefully the tests will pass.
I'd still prefer to keep this in draft until I receive the multichannel example. (so that I can try and see if there is anything else to modify)

[weiglszonja]

Notes for Bruker version (can be checked in the XML file)

• files that were created with version 5.6.64 are individual .ome.tif files (dual plane example, single color example)
• files that were created with version 5.8.64 are multipage .ome.tif files (dual color example here)
  The number of files for the multipage tiffs can depend on the number of channels, but I also think there can be more files per channel depending on the chunk size that was used (e.g. ~500MB). Also possible that even with the new version the user can choose to create individual tiffs, but that is being confirmed here.

Adding @h-mayorquin to this thread as he is also working with dual channel data.

[CodyCBakerPhD]

Unfortunately it looks like @h-mayorquin's data, though it was originally Bruker output, was converted into another format (nifty) after acquisition (and source was not kept) so the example data we have here is from Pinto lab and the NWB helpdesk (best volumetric example so far)

[CodyCBakerPhD]

LGTM! Thanks for all the hard work on this

[codecov]

Codecov Report

Merging #230 (31bb80a) into main (b7c6048) will increase coverage by 0.98%.
The diff coverage is 96.29%.

❗ Current head 31bb80a differs from pull request most recent head 16a606c. Consider uploading reports for the commit 16a606c to get more accurate results

@@            Coverage Diff             @@
##             main     #230      +/-   ##
==========================================
+ Coverage   76.15%   77.13%   +0.98%     
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  Files          37       37              
  Lines        2583     2725     +142     
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+ Hits         1967     2102     +135     
- Misses        616      623       +7     

Flag	Coverage Δ
unittests	77.13% <96.29%> (+0.98%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
...iffimagingextractors/brukertiffimagingextractor.py	97.00% <96.29%> (-0.82%)	⬇️

... and 1 file with indirect coverage changes