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Merged
merged 51 commits into from
Aug 4, 2025
Merged

MAJOR REFACTOR: removes Curation table, new metadata ingestion & visualizations #64

merged 51 commits into from
Aug 4, 2025
+634 −413

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@kushalbakshi
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@kushalbakshi kushalbakshi commented Aug 4, 2025 •
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To do after merge and before next release:

  • Remove external store tables and code
  • Increment version
  • Update CHANGELOG

kushalbakshi and others added 30 commits June 18, 2024 13:20
@kushalbakshi
Update(setup.py) element-interface branch to resolve installation con…
7cfc720 
…flicts
@kushalbakshi
Ingest Inscopix metadata
589f3d3
@kushalbakshi
Fix(miniscopy.py) TypeError
63dccf6
@kushalbakshi
Remove CaImAn install from setup.py
2149c8c
@kushalbakshi
Update tables in miniscope schema + update devcontainer for codespaces
2d7418b
@kushalbakshi
Attempt caiman install from dockerfile during devcontainer build
e9ba34f
@kushalbakshi
Clone and install caiman in image build
715fed7
@kushalbakshi
Install caiman in the devcontainer image
b954899
@kushalbakshi
Update devcontainer to python 3.10
dd4a397
@kushalbakshi
Fix(devcontainer.json) imaging -> miniscope
d321be1
@kushalbakshi
Merge branch 'dev_update_element' of https://github.com/kushalbakshi/…
b39fe9e 
…element-miniscope into dev_update_element
@kushalbakshi
Update PYTHON_VERSION env
914a55d
@kushalbakshi
Merge branch 'dev_update_element' of https://github.com/kushalbakshi/…
46d6d61 
…element-miniscope into dev_update_element
@kushalbakshi
Create no_curation module
a393a38
@kushalbakshi
Update with changes from code review and testing
b566fd9
@kushalbakshi
Apply Black formatting
80845ef
@kushalbakshi @ttngu207
Update element_miniscope/miniscope_no_curation.py
9afedbb 
Co-authored-by: Thinh Nguyen <[email protected]>
@kushalbakshi
Remove updated key_source for Processing table
e5358cb
@ttngu207
Merge pull request #1 from kushalbakshi/dev-no_curation
80edb0f 
Remove curation + update Element for improved compatibility with 2p
@kushalbakshi
Update foreign key reference in miniscope_report
42c52bd
@ttngu207
Merge pull request #2 from kushalbakshi/dev-no_curation
2cc011b 
Update foreign key reference in `miniscope_report`
@kushalbakshi
Fix(miniscope_no_curation.py) session directory handling in `infer_ou…
05b36a7 
…tput_dir()`
@ttngu207
Merge pull request #3 from kushalbakshi/dev-no_curation
50cd72b 
Fix session directory handling when inferring output dir
@kushalbakshi
Remove input hash generation in Processing
1603fb7
@ttngu207
Merge pull request #4 from kushalbakshi/dev-no_curation
e8c9a19 
Remove input hash generation in `Processing`
@kushalbakshi
Remove redundant as_posix() for output_dir
0fdd66f
@kushalbakshi
Merge pull request #5 from kushalbakshi/dev-no_curation
aee699b 
Remove redundant `as_posix()` for output_dir
@kushalbakshi
Change Curation to ProcessingTask in get_loader_result()
52fae0f
@kushalbakshi
insert() -> `insert1() for MotionCorrection.Summary
a7d6b9c
@ttngu207
Merge pull request #6 from kushalbakshi/dev-no_curation
bde3414 
Change `Curation` to `ProcessingTask` in `get_loader_result()`
kushalbakshi and others added 21 commits August 12, 2024 10:39
@kushalbakshi
Fix fluo_channel -> fluorescence_channel
0a4ecdc
@kushalbakshi
Merge pull request #7 from kushalbakshi/dev-no_curation
898de79 
Fix fluo_channel -> fluorescence_channel
@kushalbakshi
Add external store to Processing table + minor updates
72ee46b
@kushalbakshi
ignore extra fields for Processing.File
7018ae0
@kushalbakshi
feat(cell_plot.py): Summary image plotting functions
5c51e42
@kushalbakshi
Add __init__.py
e360d19
@kushalbakshi
feat(cell_plot.py): Simplify overlayed image function
4859463
@kushalbakshi
Remove virtual module creation
a2d0545
@kushalbakshi
Fix names in figure dropdown
3abe10c
@kushalbakshi
Use HSV masks
9608f76
@kushalbakshi
Add defailt value for processing_output_dir
29d5bfb
@kushalbakshi
Revert to using heatmap for JSON compatibility
bb89d67
@ttngu207
feat(miniscope_report): miniscope_report no longer auto imported/ac…
ae1a47f 
…tivate if not used
@kushalbakshi
Merge pull request #1 from ttngu207/patch-1
8efe848 
feat(miniscope_report): `miniscope_report` no longer auto imported/activate if not used
@kushalbakshi
Fetch mask weights for figure data
3d49aad
@kushalbakshi
Merge branch 'fmi_luthi' of https://github.com/kushalbakshi/element-m…
0b89ed3 
…iniscope into fmi_luthi
@kushalbakshi
bugfix in plot_cell_overlayed_image
23e454a
@kushalbakshi
Revert name to miniscope from miniscope_no_curation. Add alias
5dc893a
@kushalbakshi
Apply Black formatting
3f83147
@kushalbakshi @ttngu207
Update element_miniscope/miniscope_report.py
7f056fa 
Co-authored-by: Thinh Nguyen <[email protected]>
@ttngu207
Merge pull request #63 from kushalbakshi/dev_new-main
0710578 
MAJOR REFACTOR: Updates to metadata ingestion, store CaImAn outputs to external store, new visualizations
@kushalbakshi kushalbakshi requested a review from ttngu207 August 4, 2025 17:24
@MilagrosMarin MilagrosMarin self-requested a review August 4, 2025 17:29
@MilagrosMarin MilagrosMarin merged commit fa34422 into main Aug 4, 2025
2 checks passed
@kushalbakshi kushalbakshi mentioned this pull request Aug 4, 2025
Merged
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@MilagrosMarin MilagrosMarin MilagrosMarin approved these changes

@ttngu207 ttngu207 ttngu207 approved these changes

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@kushalbakshi @MilagrosMarin @ttngu207