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Curated clustering heavy load #25

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Risker202 wants to merge 81 commits into from
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Curated clustering heavy load #25

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0229105
feat: make `create_neuropixels_probe` a separate step (not part of ac…
ttngu207 May 8, 2024
5881d6c
Merge branch 'dev_separated_create_probe' into nei_nienborg
ttngu207 May 8, 2024
76078c9
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 May 8, 2024
214708c
feat: update ephys for nienborglab pipeline
ttngu207 May 9, 2024
5f69808
Merge branch 'dev_spikeinterface_v101' into nei_nienborg
ttngu207 Jun 4, 2024
988ca7b
Merge pull request #1 from ttngu207/nei_nienborg
kushalbakshi Jun 4, 2024
5349f4f
feat: add `get_sync_ephys_function` for ephys sync
ttngu207 Jun 13, 2024
162abb9
chore: remove the irrelevant ephys modules
ttngu207 Jun 13, 2024
747f09d
Merge pull request #2 from ttngu207/nei_nienborg
ttngu207 Jun 13, 2024
e5fea7f
feat: add LFP ingestion for Trellis (ns2)
ttngu207 Jun 28, 2024
3149825
Merge pull request #3 from ttngu207/nei_nienborg
kushalbakshi Jun 28, 2024
4b0a31a
Merge branch 'dev_spikeinterface_v101' into nei_nienborg
ttngu207 Jul 5, 2024
ee58336
Merge pull request #4 from ttngu207/nei_nienborg
ttngu207 Jul 5, 2024
e7933de
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 Jul 5, 2024
5db8e4d
Merge pull request #5 from ttngu207/nei_nienborg
ttngu207 Jul 5, 2024
95a7e15
fix: add extractors import
ttngu207 Jul 6, 2024
82776bd
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 Jul 6, 2024
27efdc9
Merge pull request #6 from ttngu207/nei_nienborg
ttngu207 Jul 6, 2024
a44f976
fix: recording_extractor_full_dict is deprecated (https://github.com/…
ttngu207 Jul 6, 2024
5f2e17d
Merge pull request #7 from ttngu207/nei_nienborg
ttngu207 Jul 6, 2024
7d6433a
Merge branch 'datajoint-spikeinterface' of https://github.com/dj-scio…
kushalbakshi Aug 7, 2024
885feb8
Update element-interface requirement to `staging`
kushalbakshi Aug 7, 2024
554d3e3
Merge pull request #8 from kushalbakshi/nei_nienborg
ttngu207 Aug 7, 2024
8aba9ea
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 Aug 22, 2024
26d6713
Merge branch 'nei_nienborg' into datajoint-spikeinterface
ttngu207 Aug 22, 2024
03193b1
Merge pull request #11 from dj-sciops/datajoint-spikeinterface
ttngu207 Aug 22, 2024
1004895
Merge pull request #9 from ttngu207/nei_nienborg
ttngu207 Aug 22, 2024
8c444b7
Added fix to make phy export overwrite if the phy folder already exists
ttngu207 Oct 1, 2024
5e78ba3
feat(sorting): add `File` to store result files as `filepath@store`
ttngu207 Oct 1, 2024
3befdfe
Merge pull request #10 from ttngu207/nei_nienborg
ttngu207 Oct 1, 2024
d7e53d0
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 Oct 9, 2024
5db58e8
Merge pull request #11 from ttngu207/nei_nienborg
ttngu207 Oct 9, 2024
486e4a2
Merge branch 'datajoint-spikeinterface' into nei_nienborg
ttngu207 Oct 9, 2024
830f32a
Merge pull request #12 from ttngu207/nei_nienborg
ttngu207 Oct 9, 2024
180fbc6
feat: add `File` part table for external storage
ttngu207 Dec 3, 2024
2589c67
update: handles channel indices from multi-probe channel-concatenated…
ttngu207 Jan 21, 2025
ff8890b
Merge pull request #14 from ttngu207/nei_nienborg
kushalbakshi Jan 21, 2025
af3dde5
feat: update handling new channel-mapping scheme for CuratedClusterin…
ttngu207 Jan 23, 2025
1262f21
Merge pull request #15 from ttngu207/nei_nienborg
kushalbakshi Jan 23, 2025
f1b01a7
feat: corresponding update to channel mapping for waveform
ttngu207 Jan 24, 2025
19b5018
Merge pull request #16 from ttngu207/nei_nienborg
ttngu207 Jan 24, 2025
e096ac4
Merge branch 'main' into dev_new_main_external-storage
ttngu207 Feb 13, 2025
4a5396d
Merge branch 'main' into dev_new_main_external-storage
ttngu207 Feb 14, 2025
269f3f2
Merge remote-tracking branch 'upstream/main' into dev_new_main_extern…
ttngu207 Feb 14, 2025
4402567
Merge pull request #216 from ttngu207/main_external-storage
ttngu207 Feb 14, 2025
1522cb5
install neo from source until 0.14.1 release
ttngu207 Mar 5, 2025
460e7ec
fix: temporary version pin to resolve int overflow issue
ttngu207 Mar 5, 2025
af984b8
Merge pull request #219 from datajoint/main
ttngu207 May 13, 2025
9aaf2dc
chore: temp fix spikeinterface issue 251
ttngu207 Jul 5, 2025
bfd84ed
Merge pull request #16 from datajoint/main_external-storage
ttngu207 Jul 5, 2025
9e45a67
chore: insert `File` one by one to avoid timeout
ttngu207 Jul 7, 2025
f34ea70
chore: minor spikeinterface temp branch name fix
ttngu207 Jul 7, 2025
7bce985
Use `spikeinterface` `main` branch instead of feature branch - issue …
ttngu207 Nov 5, 2025
481f77b
Merge pull request #226 from ttngu207/main_external-storage
kushalbakshi Nov 5, 2025
098839d
Merge branch 'main_external-storage' of https://github.com/datajoint/…
ttngu207 Nov 21, 2025
f9ed551
Remove version pinning for `neo` and `spikeinterface`
ttngu207 Dec 4, 2025
a852ae7
feat: use three-part-make for `EphysRecording` table
ttngu207 Dec 5, 2025
1e68b86
Merge branch 'main_external-storage' of https://github.com/dj-sciops/…
ttngu207 Dec 5, 2025
bda31e0
fix: update probe model assignment in SpikeGLXMeta class
ttngu207 Dec 5, 2025
d97e6a7
feat: handle/concat multiple spikeglx bin files at PreProcessing
ttngu207 Dec 5, 2025
a9c4559
feat: implement ephys curation functionality with manual curation
ttngu207 Dec 8, 2025
b6cfaf6
Merge pull request #18 from dj-sciops/main
ttngu207 Dec 10, 2025
f4a431b
feat: add ManualLabel part to CuratedClustering for manual unit labeling
ttngu207 Dec 20, 2025
1dd8679
Merge branch 'main_external-storage' of https://github.com/dj-sciops/…
ttngu207 Dec 20, 2025
8f46414
Fix KeyError in ApplyOfficialCuration.make for multi-insertion probes
Jan 20, 2026
45fb84f
Merge pull request #19 from dj-sciops/fix/curation-channel-mapping
kushalbakshi Feb 9, 2026
9904b6e
Merge pull request #21 from dj-sciops/main
ttngu207 Feb 9, 2026
7733c3c
Fix ApplyOfficialCuration.make to resolve curation_id from OfficialCu…
ttngu207 Feb 9, 2026
2649cf4
Merge pull request #22 from dj-sciops/fix/official-curation-key-resol…
ttngu207 Feb 9, 2026
afc7cec
Fix electrode_map to exclude channel_idx before unit insert
ttngu207 Feb 10, 2026
12bdd13
Merge pull request #23 from dj-sciops/fix/electrode-map-channel-idx
ttngu207 Feb 10, 2026
f08475c
feat: Add Kilosort 4 to ephys.ClusteringMethod lookup table
Feb 23, 2026
c53eac5
feat: Add functionality to infer channel map for microwire brush arrays
Feb 23, 2026
c37d3b6
Small fix to infer_map.py
Feb 23, 2026
366b291
feat: Add new preprocessing method: MBA_infer_map (si_preprocessing.py)
Feb 23, 2026
1860065
small fix to si_preprocessing.py
Feb 23, 2026
5d077d9
feat: Mild refactor to si_spike_sorting.PreProcessing.make to allow e…
Feb 23, 2026
a8614f8
refactor: Add default scale params to infer_map
Feb 23, 2026
9113cda
Tiny refactor of scale_map, to catch extra scale parameters (infer_ma…
Feb 24, 2026
254d4ff
Merge pull request #24 from Risker202/infer_map
ttngu207 Feb 24, 2026
7822a74
refactor: DRAFT: Alter CuratedClustering.make to handle insertion of …
Apr 1, 2026
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