Spikeinterface - #11

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abisi wants to merge 77 commits into

mainfrom

Commits on Dec 17, 2024

add toml and repackage
JulesLebert
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3df7c48
allow catgt to run on linux
JulesLebert
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82a641b

Commits on Dec 20, 2024

Allow multiple spikesorters + run bombcell
JulesLebert
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f0fb672

Commits on Jan 8, 2025

preprocessing pipeline
JulesLebert
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232fc52

Commits on Jan 23, 2025

Commits on Feb 10, 2025

use of spikeinterface artifact correction instead of custom one
JulesLebert
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7407308
running version of the full pipeline
JulesLebert
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f2eac2b

Commits on Feb 17, 2025

Addind overstrike and allow artifact correction before and after the artifact time
JulesLebert
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aca8ffe

Commits on Sep 1, 2025

working pipeline
JulesLebert
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f9cbb80

Commits on Jan 23, 2026

update kilosort4 and changed bomcell to py_bombcell in the main script
JulesLebert
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3cc0bf1

Commits on Jan 28, 2026

do drift correction outside of kilosort
JulesLebert
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644e97d

Commits on Feb 5, 2026

add sync to container
JulesLebert
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e4cfaec

Commits on Mar 31, 2026

add context offset extraction from catgt
JulesLebert
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c77696f
add singularity scripts
JulesLebert
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dd78d54

Commits on Apr 1, 2026

add pybombcell
JulesLebert
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fbcb971

Commits on Apr 7, 2026

added ibl_atlas data reformating for ephys alignment (from Axel)
JulesLebert
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ab154a7
context offset extraction with catgt + configs for parallel GPU jobs
Jules Lebert
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3c84d2f
edit spikesorting slurm serial job
Jules Lebert
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7a915fa
updated readme
Jules Lebert
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8368674
update README
Jules Lebert
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88c4932

Commits on Apr 27, 2026

merged
abisi
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235c2e1

Commits on Apr 28, 2026

WIP spikeinterface branch pre-merge work
abisi
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89d8d63
WIP spikeinterface: DREDge standalone for motion estimation + slurm script for jed + script for ephys data to process detection + some minor updates for paths
abisi
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875ffc1
readme for data transfer
abisi
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a27e8b7
update README command for copying
abisi
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d4942e6
update README setup
abisi
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1f033a5
update README scitas
abisi
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6562039
update README scitas
abisi
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8463e8c

Commits on Apr 29, 2026

WIP: dredge stuff, kuma script config + pybombcell with ephys prop
abisi
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f426ec4
drift GUI by Mayo Faulkner
abisi
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f0822d9
info on channel used for artifact times correction - setup dependent
abisi
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f846232
minor comment
abisi
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86aa867
dredge config used from yaml
abisi
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fe1131d
fix dredge config
abisi
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bfffe9e

Commits on Apr 30, 2026

INFO: hard-fix for dredge with copy of SI extractor class
abisi
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f0763f9

Commits on May 1, 2026

paths handling
abisi
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026c4b2
dredge scripts update
abisi
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801c989

Commits on May 8, 2026

legacy local script path update + script for motion estimation analysis
abisi
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933100f
comment fix
abisi
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2b4cc32

Commits on May 10, 2026

minor change
abisi
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234aed7
script to plot and analyze probe motion across dataset
abisi
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c84f02d

Commits on May 11, 2026

update probe drift dataset summary
abisi
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2f1a601
update drift GUI with raw trace, viz improvements and interactive intervals
abisi
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0adac0d

Commits on May 13, 2026

update configs for anatomy and do filters
abisi
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9467b0f
update main process_si script
abisi
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86b993f
probe ordering + paths managements + gain_to_uv hardcoded for bombcell + minor things
abisi
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fc0488b
drift gui - option to choose which KS output
abisi
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cdda434
more data transfer doc
abisi
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e248f23
switched order mean wf and wf plotting + tprime fix + transfer command fix + utils name chnage
abisi
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2b4467e
minor
abisi
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e47b183

Commits on May 15, 2026

WIP LF band extractor for NP2 recordings
abisi
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6df610d

Commits on May 18, 2026

WIP date filtering + update ephys utils + update filtering detect files script + test SI exporter to IBL GUI + band extraction LF / shanks
abisi
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1848589

Commits on May 20, 2026

update paths + pybombcell default params no presence ratio + catgt filters and lf split
abisi
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bb0abb9

Commits on May 21, 2026

fix bombcell presence ratio setting and detect ephys script
abisi
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59b8991

Commits on May 28, 2026

update drift motion whole-dataset analysis
abisi
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350e747

Commits on May 29, 2026

analysis of drift and spike sorting outputs
abisi
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840ea1e
dredge utils: larger plot + commented CatGT-like processing
abisi
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1512416
cleanup run_sorter
abisi
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8a492bb

Commits on Jun 2, 2026

updated name for more general
abisi
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ff2b7c5
minor updates for AB MH
abisi
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e0692dd

Commits on Jun 5, 2026

update path checks and details
abisi
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74c5818