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Update Suite2pSegmentationInterface to support multiple channels and planes #601

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merged 52 commits into from
Dec 1, 2023

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weiglszonja
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@weiglszonja weiglszonja commented Oct 17, 2023

@weiglszonja weiglszonja marked this pull request as draft October 17, 2023 12:21
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Noticed an issue with the extractor, as it overrides the channel_name to "OpticalChannel" or capitalised version of the original channel name (chan1 or chan2) to use it for the name of the OpticalChannel it will be created, the override results in incorrect read for the mean image, fixed in:
catalystneuro/roiextractors#263

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@weiglszonja @alessandratrapani Will be pushing for a new roiextractors release tomorrow; is this PR ready to go once that happens?

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@CodyCBakerPhD on my end it is, I just listed @alessandratrapani for review

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It looks all right to me

@weiglszonja weiglszonja marked this pull request as ready for review December 1, 2023 15:38
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codecov bot commented Dec 1, 2023

Codecov Report

Merging #601 (f8ecf3c) into main (3c614b9) will increase coverage by 0.07%.
Report is 3 commits behind head on main.
The diff coverage is 98.41%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #601      +/-   ##
==========================================
+ Coverage   91.73%   91.80%   +0.07%     
==========================================
  Files         108      108              
  Lines        5712     5762      +50     
==========================================
+ Hits         5240     5290      +50     
  Misses        472      472              
Flag Coverage Δ
unittests 91.80% <98.41%> (+0.07%) ⬆️

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

Files Coverage Δ
src/neuroconv/tools/importing.py 74.28% <100.00%> (+6.42%) ⬆️
...euroconv/tools/nwb_helpers/_models/_hdf5_models.py 62.50% <100.00%> (ø)
...c/neuroconv/tools/spikeinterface/spikeinterface.py 93.11% <100.00%> (-0.02%) ⬇️
src/neuroconv/tools/testing/mock_ttl_signals.py 100.00% <100.00%> (ø)
...tainterfaces/ophys/suite2p/suite2pdatainterface.py 98.00% <97.87%> (-2.00%) ⬇️

... and 2 files with indirect coverage changes

@CodyCBakerPhD CodyCBakerPhD merged commit 9da6dcb into main Dec 1, 2023
47 checks passed
@CodyCBakerPhD CodyCBakerPhD deleted the update_Suite2P_multiplane branch December 1, 2023 16:26
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3 participants