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Image processing / segmentation on a per-field basis #186

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wants to merge 75 commits into from
Closed

Image processing / segmentation on a per-field basis #186

wants to merge 75 commits into from

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ttngu207
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@ttngu207 ttngu207 commented Mar 8, 2024 •
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Create a new schema field_processing to handle Calcium image processing on a per-field basis.
Primary use case is to handle the processing for mesoscope data
Provide flexibility to add preprocessing/postprocessing steps to the processing/analysis of each field.

Thinh Nguyen and others added 30 commits August 16, 2023 18:32
support multiplane processing with CaImAn - per-plane basis
5d71dab
update pipeline to support per-plane processing with caiman
53a75b8
at Processing - generate new PerPlaneProcessingTask or confirm all Pe…
34f2351 
…rPlaneProcessing have completed
Update setup.py
d471a04
bugfix
23e6527
minor fix
187522b
@kushalbakshi
Update attribute channel=' ' -> channel=null
02e87f0
@kushalbakshi
Update aggr function with .proj()
54dbf3a
@kushalbakshi
Update key_source for Processing
bfc1125
update caiman results ingestion - use latest caiman loader
b7c9e05
Update version.py
a0bb444
@kushalbakshi
Revert Processing ker_source + fix output_dir error
b2961f6
@kushalbakshi
Update key_source logic for Processing
6d03f94
@kushalbakshi
Fix for str AttributeError
38021f3
@kushalbakshi
Fix TypeError for 'str' and 'str'
e6d4c5b
@kushalbakshi
Debug mkdir AttributeError
16d4573
@kushalbakshi
Update caiman_loader keys for motion correction
3cb8b70
@kushalbakshi
Remove mask classification extraction from caiman loader
c12e7bb
@kushalbakshi
Merge branch 'per-plane-processing' of https://github.com/ttngu207/el…
07de08b 
…ement-calcium-imaging into per-plane-processing
@kushalbakshi
Add exception to debug summary images
a499fed
@kushalbakshi
Refine summary image loading
9322f77
@kushalbakshi
Internal variable fkey -> field_key
a57a024
@kushalbakshi
Append to summary image list
a645be4
fix incorrect shape in summary images retrieval
bf48a58
@kushalbakshi
Manually merge changes from Thinh's branch
342b86f
@kushalbakshi @ttngu207
Update element_calcium_imaging/imaging_no_curation.py
e7320b3 
Co-authored-by: Thinh Nguyen <[email protected]>
@ttngu207
Merge pull request #2 from kushalbakshi/per-plane-processing
87b180f
@kushalbakshi
Merge pull request datajoint#161 from ttngu207/per-plane-processing
40ac3c2 
Per plane processing
Merge branch 'main' of https://github.com/datajoint/element-calcium-i…
328393a 
…maging into per-plane-processing
@sidhulyalkar
Merge pull request datajoint#163 from ttngu207/per-plane-processing
8e9178e 
pull from upsteam main
sidhulyalkar and others added 24 commits October 16, 2023 16:41
@sidhulyalkar
Merge pull request datajoint#172 from kushalbakshi/per-plane-processing
7651d35 
Revert old `slice` commit
@kushalbakshi
Merge branch 'staging' into caiman_per_plane_processing
b565204
feat(imaging): write bigtiff for caiman processing for bruker files
a5b2e89
Merge remote-tracking branch 'upstream/caiman_per_plane_processing' i…
087c10b 
…nto per-plane-processing
style(imaging)
50b3754
update(setup): revert bad merge conflict
bce6edf
@kushalbakshi
Merge pull request datajoint#178 from ttngu207/per-plane-processing
3c02d12 
feat(imaging): write bigtiff for caiman processing for bruker files
@kushalbakshi
Fix - Remove plane_idx from write_single_bigtiff() for caiman pro…
4dc70a8 
…cessing
@kushalbakshi
Update requirements in setup.py
0ef9b60
@kushalbakshi
Update element-interface requirement to staging branch
d49f14e
Merge pull request datajoint#180 from kushalbakshi/per-plane-processing
31bf615 
Fix - Remove `plane_idx` from `write_single_bigtiff()`
Merge pull request #4 from datajoint/caiman_per_plane_processing
bc63a6e 
pull from upstream
Merge branch 'main' of https://github.com/datajoint/element-calcium-i…
f32dd8d 
…maging into per-plane-processing
fix(setup): fix incorrect merge conflict resolution
89a39be
fix(setting): black formatting
d40da2a
Merge pull request datajoint#182 from ttngu207/per-plane-processing
3c816e4 
Fix merge conflict
@kushalbakshi
Merge pull request datajoint#183 from datajoint/caiman_per_plane_proc…
a719726 
…essing

Caiman per plane processing
feat(imaging): make output_dir if not exist for task_mode="trigger"
07087fa
fix(scan): bugfix ingesting field xyz for mesoscan (multiROI) from Sc…
a8f9009 
…anImage
@ttngu207
feat(field_processing): implement separate flow of processing for eac…
6d06194 
…h scan field
@ttngu207
Update field_processing.py
6e9b9cb
@ttngu207
feat: add FieldPostProcessing
26cbacf
@ttngu207
Update field_processing.py
ece145c
@ttngu207
fix: update key_source, update FieldPostProcessing
f1bbafb
@ttngu207 ttngu207 marked this pull request as ready for review March 18, 2024 22:26
@ttngu207 ttngu207 closed this Mar 19, 2024
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@kushalbakshi kushalbakshi Awaiting requested review from kushalbakshi

@dimitri-yatsenko dimitri-yatsenko Awaiting requested review from dimitri-yatsenko

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3 participants
@ttngu207 @kushalbakshi @sidhulyalkar