Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Caiman per plane processing #183

Merged
merged 65 commits into from
Feb 1, 2024
Merged

Caiman per plane processing #183

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
65 commits
Select commit Hold shift + click to select a range
5d71dab
support multiplane processing with CaImAn - per-plane basis
Aug 16, 2023
53a75b8
update pipeline to support per-plane processing with caiman
Aug 23, 2023
34f2351
at Processing - generate new PerPlaneProcessingTask or confirm all P…
Aug 23, 2023
d471a04
Update setup.py
Aug 23, 2023
23e6527
bugfix
Aug 23, 2023
187522b
minor fix
Aug 24, 2023
02e87f0
Update attribute `channel=' '` -> `channel=null`
kushalbakshi Aug 24, 2023
54dbf3a
Update `aggr` function with `.proj()`
kushalbakshi Aug 24, 2023
bfc1125
Update `key_source` for `Processing`
kushalbakshi Aug 24, 2023
b7c9e05
update caiman results ingestion - use latest caiman loader
Aug 25, 2023
a0bb444
Update version.py
Aug 25, 2023
b2961f6
Revert `Processing` ker_source + fix output_dir error
kushalbakshi Aug 25, 2023
6d03f94
Update key_source logic for `Processing`
kushalbakshi Aug 25, 2023
38021f3
Fix for str AttributeError
kushalbakshi Aug 25, 2023
e6d4c5b
Fix TypeError for 'str' and 'str'
kushalbakshi Aug 25, 2023
16d4573
Debug mkdir AttributeError
kushalbakshi Aug 25, 2023
3cb8b70
Update caiman_loader keys for motion correction
kushalbakshi Aug 29, 2023
c12e7bb
Remove mask classification extraction from caiman loader
kushalbakshi Aug 29, 2023
07de08b
Merge branch 'per-plane-processing' of https://github.com/ttngu207/el…
kushalbakshi Aug 29, 2023
a499fed
Add exception to debug summary images
kushalbakshi Aug 29, 2023
9322f77
Refine summary image loading
kushalbakshi Aug 29, 2023
a57a024
Internal variable fkey -> field_key
kushalbakshi Aug 29, 2023
a645be4
Append to summary image list
kushalbakshi Aug 29, 2023
bf48a58
fix incorrect shape in summary images retrieval
Aug 29, 2023
342b86f
Manually merge changes from Thinh's branch
kushalbakshi Aug 30, 2023
e7320b3
Update element_calcium_imaging/imaging_no_curation.py
kushalbakshi Aug 30, 2023
87b180f
Merge pull request #2 from kushalbakshi/per-plane-processing
ttngu207 Aug 30, 2023
40ac3c2
Merge pull request #161 from ttngu207/per-plane-processing
kushalbakshi Sep 5, 2023
328393a
Merge branch 'main' of https://github.com/datajoint/element-calcium-i…
Sep 5, 2023
8e9178e
Merge pull request #163 from ttngu207/per-plane-processing
sidhulyalkar Sep 5, 2023
03f4b5e
update get_calcium_imaging_files parameter
sidhulyalkar Sep 6, 2023
7fd7c40
Merge branch 'main' of https://github.com/sidhulyalkar/element-calciu…
sidhulyalkar Sep 6, 2023
b9a590d
Merge branch 'main' into per-plane-processing
Sep 6, 2023
7f1c596
code cleanup
Sep 6, 2023
2cf78bb
Merge pull request #165 from ttngu207/per-plane-processing
kushalbakshi Sep 6, 2023
1a8bc68
Update setup.py
Sep 6, 2023
70f2a84
Fix `PrairieViewMeta` import statements
kushalbakshi Sep 7, 2023
69831b2
Black formatting
kushalbakshi Sep 7, 2023
649fe4a
Merge pull request #166 from kushalbakshi/per-plane-processing
sidhulyalkar Sep 7, 2023
85718e5
hard set force_sktiff to true
sidhulyalkar Sep 7, 2023
4b15184
merge upstream
sidhulyalkar Sep 7, 2023
580d9ee
bump version
sidhulyalkar Sep 7, 2023
83b27a3
Merge pull request #167 from sidhulyalkar/caiman_per_plane_processing
kushalbakshi Sep 7, 2023
b30ac91
Add motion correction indicies to caiman params
kushalbakshi Oct 12, 2023
003c312
Black formatting
kushalbakshi Oct 12, 2023
d5f6a1d
Merge branch 'caiman_per_plane_processing' of https://github.com/data…
kushalbakshi Oct 16, 2023
8b33b76
Fix typo indicies -> indices
kushalbakshi Oct 16, 2023
139f5bb
Merge pull request #171 from kushalbakshi/per-plane-processing
sidhulyalkar Oct 16, 2023
c45ee5d
Revert old `slice` commit
kushalbakshi Oct 16, 2023
7651d35
Merge pull request #172 from kushalbakshi/per-plane-processing
sidhulyalkar Oct 16, 2023
b565204
Merge branch 'staging' into caiman_per_plane_processing
kushalbakshi Nov 28, 2023
a5b2e89
feat(imaging): write bigtiff for caiman processing for bruker files
Jan 29, 2024
087c10b
Merge remote-tracking branch 'upstream/caiman_per_plane_processing' i…
Jan 29, 2024
50b3754
style(imaging)
Jan 29, 2024
bce6edf
update(setup): revert bad merge conflict
Jan 29, 2024
3c02d12
Merge pull request #178 from ttngu207/per-plane-processing
kushalbakshi Jan 29, 2024
4dc70a8
Fix - Remove `plane_idx` from `write_single_bigtiff()` for caiman pro…
kushalbakshi Feb 1, 2024
0ef9b60
Update requirements in `setup.py`
kushalbakshi Feb 1, 2024
d49f14e
Update element-interface requirement to `staging` branch
kushalbakshi Feb 1, 2024
31bf615
Merge pull request #180 from kushalbakshi/per-plane-processing
Feb 1, 2024
bc63a6e
Merge pull request #4 from datajoint/caiman_per_plane_processing
Feb 1, 2024
f32dd8d
Merge branch 'main' of https://github.com/datajoint/element-calcium-i…
Feb 1, 2024
89a39be
fix(setup): fix incorrect merge conflict resolution
Feb 1, 2024
d40da2a
fix(setting): black formatting
Feb 1, 2024
3c816e4
Merge pull request #182 from ttngu207/per-plane-processing
Feb 1, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions .vscode/settings.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@
"editor.rulers": [
88
],
"python.formatting.provider": "none",
"python.formatting.provider": "black",
"[python]": {
"editor.defaultFormatter": "ms-python.black-formatter"
"editor.defaultFormatter": null
},
"[markdown]": {
"editor.defaultFormatter": "disable"
Expand Down
Loading
Loading