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Photometry integration #938

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Photometry integration #938

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@grg2rsr grg2rsr commented Feb 24, 2025

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mayofaulkner and others added 30 commits December 18, 2024 10:25
@mayofaulkner
Merge branch 'release/3.2.0' into develop
7295c07
@themattinthehatt
add motion energy to LP task
4d208b4
@themattinthehatt
bugfix
178e0f9
@themattinthehatt
remove unnecessary comments
0b144d6
@themattinthehatt
flake
d138737
@oliche
allow none labels in plot insertions
c3962f7
@oliche
rename spike sorting log
e81480b
@oliche
spike sorting log in alf collection for task signature
558bde4
@oliche
add waveform datasets to the spike sorting task signature
6c37263
@oliche
spike sorting loader default switched to iblsorter
ea32cae
@oliche
remove temporary folder before waveform extraction to clear some space
f6b54c4
@oliche
add iblsorter log to the alf folder
1d0107c
@oliche
on GPU lock found, raise if task mode is set to raise
b9b074d
@oliche
patcher: add context to registration exception
1834891
@oliche
flake
375c7c5
@oliche
check only size not hash for S3 re-runs
fed7b2e
@oliche
setup logger for iblsorter
d4b3bba
@oliche
update ibl-neuropixels requirement
b520d88
@oliche
add waveform files to the output list
1d2401e
@oliche
remove duplicate files in output task
1d5bd9a
@oliche
replace ricker function that has been removed in scipy
f3f44ad
@oliche
Merge pull request #901 from int-brain-lab/aws
19c5ea5 
Aws
@mayofaulkner
update environment for litpose task
493d8bc
@grg2rsr
updated requirements, updated pipelines
06b0478
@mayofaulkner
add in slices kwarg to pass into suite2p params
b4b4787
@grg2rsr
fibers are now named fiber_{brain_region} in the extraction process
bff5469
@mayofaulkner
add default n_ephys value to criterion delay
362d590
@mayofaulkner
unpack criteria
9b962bd
@mayofaulkner
catch error for displaying info
bad825d
@oliche
Merge branch 'develop' into litpose
c519313
oliche and others added 26 commits January 21, 2025 10:11
@oliche
avoid dummy package for iblqt
745f668
@oliche
Merge pull request #900 from int-brain-lab/litpose
caa8562 
Add motion energy computation to LightningPose task
@oliche
plot to create a star plot
d49cb2b
@oliche
most of the time it doesn´t make sense to have a different origin than 0
7c9212d
@mayofaulkner
ensure sparse_npz files are registered
399bd94
@oliche
Merge pull request #917 from int-brain-lab/starplot
27c5a36 
plot to create a star plot
@oliche @k1o0
One3 (#926)
c2aecb6 
* set ONE on the v3 branch

* auto -> remote mode; fix unit tests and imports

* fix the version reading from log bug

* Fix brainbox.io tests - flake

* set ONE on the latest v3.0.0 branch

* bump ONE requirement after release

---------

Co-authored-by: Miles Wells <[email protected]>
@mayofaulkner
correct positions
e34ae46
@k1o0
Support for UUID objects in Notes
473236a
@mayofaulkner
Merge branch 'develop' into mesoscope_multidepth
e45c63f
@mayofaulkner
Merge branch 'develop' into docs
f0c2ada
@k1o0
Fix error in MesoscopeCompress when compressing multiply imaging bouts
b932bc9 
Resolves issue #931
@k1o0
Selectively remove old FOV datasets in MesoscopePreprocess (issue #928)
6a719c3
@mayofaulkner
update queries for ONE 3
e8a4c1e
@mayofaulkner
Merge pull request #936 from int-brain-lab/docs
74f578b 
Docs
@mayofaulkner
Merge pull request #908 from int-brain-lab/mesoscope_multidepth
5d9d63b 
add in slices kwarg to pass into suite2p params
@k1o0
Add PROJECT_EXTRACTION_VERSION and TASK_VERSION to session JSON (issue …
d604865 
…#898)
@k1o0
Remove junk IDE folder
c7a500a
@k1o0
Handle extraction of sessions where first Bpod trial missed on FPGA (…
fa6d722 
…issue #909)
@grg2rsr
fixing shifted sync timestamps in the extraction
57f7164
@grg2rsr
reading digital inputs file via iblphotometry.io (validated)
b606290
@k1o0
Update ONE version requirement
9a9ff73
@k1o0
Bump version; use ensure_list
be71131
@grg2rsr
Merge remote-tracking branch 'origin/develop' into photometry-integra…
16ffbc4 
…tion
@grg2rsr
fix for reextraction (.pqt file read instead of .csv) for digital_inp…
8ae4039 
…uts from neurophotometrics
@grg2rsr
bugfix in the extractor after fix in the experiment description file
3fd7623
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5 participants
@grg2rsr @mayofaulkner @themattinthehatt @oliche @k1o0