Origin/decoding by farznaj · Pull Request #803 · AllenInstitute/visual_behavior_analysis

Commits on Jun 25, 2020

Commits on Jun 27, 2020

manual neuropil subtraction codes added

Farzaneh Najafi
authored and
Farzaneh Najafi
committed
umap edits
Farzaneh Najafi
committed
Merge branch 'feature/clustering' of https://github.com/AllenInstitute/visual_behavior_analysis into feature/clustering
Farzaneh Najafi
committed

Commits on Jun 29, 2020

Commits on Jul 1, 2020

umap: try different parameters and plots
Farzaneh Najafi
committed
marina's clustering attempt codes added

Farzaneh Najafi
authored and
Farzaneh Najafi
committed

Commits on Jul 7, 2020

set dff and stim info for all sessions - allensdk
Farzaneh Najafi
committed
marina's codes for clustering added

Farzaneh Najafi
authored and
Farzaneh Najafi
committed

Commits on Jul 8, 2020

all_sess_dff_stim modified
Farzaneh Najafi
committed

Commits on Jul 9, 2020

add notebook
matchings
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umap: updates to notebook for creating metrics feature vector
Farzaneh Najafi
committed

Commits on Jul 10, 2020

Commits on Jul 13, 2020

add try except to multi_session_metrics creation
matchings
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Commits on Jul 21, 2020

umap and gmm codes added for the metrics feature matrix
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umap gmm codes refactoring
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Commits on Jul 22, 2020

using de-cross-talked dff traces for omission analysis
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Commits on Jul 23, 2020

svm codes updated for ct traces; some edits to omission population average codes
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scripts on the analysis computer added, related to crosstalk files, copying them, neuropil subtraction, dff computation
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svm pbs codes, minor changes
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committed
omit function: sections made clear; svm : edits
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svm init: job directory fixedgit status
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omission function: iomit (num omissions) fixed!
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Commits on Jul 31, 2020

pbs correlation codes edited for the cluster
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committed

Commits on Aug 1, 2020

bug with omit code; image surround omission
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committed
align traces on omissions for Akul
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committed

Commits on Aug 4, 2020

svm: std changed to sem for error bars; set_traces_active: bug fixed with inds_final; corr codes: some edits
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committed
summary of keras codes added
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small edits
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Commits on Aug 6, 2020

population average: baseline computation: multiple methods tried; also switching from median to mean
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Commits on Aug 7, 2020

notes file added about summary of correlation codes
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committed

Commits on Aug 10, 2020

doug and marina clustering notebooks
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committed
omission population average plotting edits
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Commits on Aug 12, 2020

umap, hdbscan clustering; svm weights saved
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committed
umap clusteirng notebooks
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committed
Merge branch 'feature/update_response_analysis' into feature/clustering
matchings
committed
adding notebooks
matchings
committed

Commits on Aug 19, 2020

minor stuff
Farzaneh Najafi
committed

Commits on Aug 20, 2020

bug fixes: image traces/peaks: some were nans, mean changed to nanmean; also sem was using all sessions, changed to non-nan sessions
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committed

Commits on Aug 21, 2020

histogram of depth and number of neurons for each planes; some other changes
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committed

Commits on Aug 25, 2020

Commits on Sep 11, 2020

old file committed
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committed

Commits on Sep 13, 2020

Merge branch 'master' into feature/clustering
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committed

Commits on Sep 22, 2020

minor
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Merge branch 'master' into feature/clustering
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committed

Commits on Sep 25, 2020

minor
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committed

Commits on Sep 28, 2020

starting the image decoding analysis
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committed

Commits on Sep 29, 2020

edits
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committed
Merge remote-tracking branch 'origin/dev' into feature/clustering
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committed

Commits on Sep 30, 2020

Merge remote-tracking branch 'origin/dev' into feature/clustering
Farzaneh Najafi
committed
Merge remote-tracking branch 'origin/dev' into feature/clustering
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committed

Commits on Oct 8, 2020

svm codes created for multi-class classification
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svm images, taking care of cluster pbs
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Commits on Oct 9, 2020

Commits on Oct 10, 2020

taking care of pbs args
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minor
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committed
session number
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committed

Commits on Oct 15, 2020

svm decoding of images; post analysis; also codes set to take slc
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committed
Merge remote-tracking branch 'origin/master' into feature/clustering
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committed
bug fix
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committed
codes modified to analyze image expectation signal
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committed

Commits on Oct 16, 2020

edits
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committed
taking care of negative values of frames svm and several other changes
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committed

Commits on Oct 20, 2020

svm images setting vars for plotting
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committed
merge
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committed
reformat.py copied from master
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committed

Commits on Oct 22, 2020

plotting codes added for svm images
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committed

Commits on Oct 23, 2020

svm images codes editws
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committed
important edits to svm main function; making it clear what's being decoded and from what. image changes also added.
Farzaneh Najafi
committed

Commits on Oct 24, 2020

bug fix
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committed
svm: important bug fix to image index of previous flash
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committed
minor
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committed
bug fix
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Commits on Oct 27, 2020

big fix; code improvement; script rename
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committed
minor
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committed

Commits on Oct 30, 2020

edits to svm images
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committed
minor
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committed

Commits on Nov 3, 2020

bug fixes to svm main code; finding overlapping rows of trials and stim df; etc
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committed

Commits on Nov 6, 2020

svm code: linking stimulus and trials dfs; adding image labels to the saved svm var file
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Commits on Nov 16, 2020

svm edits
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committed

Commits on Nov 20, 2020

correlation: control data resampled as in single beam mesoscope data
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bug fix
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Commits on Nov 24, 2020

correlation analysis: resample data to resemble single beam mesoscope; nature communications reviews
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Commits on Nov 25, 2020

svm: block by block analysis codes added
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committed

Commits on Dec 5, 2020

using initial spontaneous frames to classify omissions against
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committed

Commits on Dec 22, 2020

svm block by block analysis codes for visualization
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committed
Merge branch 'dev' into feature/clustering
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committed

Commits on Dec 23, 2020

use events for svm
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committed

Commits on Dec 24, 2020

svm fun: bug fixed for checking for the existence of all classes in the training data
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committed
edits
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Merge branch 'dev' into feature/clustering
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committed

Commits on Jan 19, 2021

svm plots codes updated to work with both whole session and block by block svm analysis
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fixing legend
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committed
Merge branch 'master' into feature/clustering
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committed

Commits on Jan 20, 2021

plotting codes updated ; minor
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minor
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Commits on Feb 8, 2021

svm engagement analysis
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Merge branch 'master' into feature/clustering
Farzaneh Najafi
committed
Merge branch 'dev' into feature/clustering
Farzaneh Najafi
committed

Commits on Feb 9, 2021

svm engagement
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Merge branch 'dev' into feature/clustering
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committed
svm engagement ready for clusgter
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committed

Commits on Feb 11, 2021

updating correlation codes to take the March 2021 data release sessions; dff; metadata still from vb dataset object
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committed
Merge branch 'dev' into feature/clustering
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committed
minor
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committed

Commits on Feb 12, 2021

correlation analysis; data release sessions
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committed
bug fix
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committed
bug fix
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bug fix
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committed
svm engagement running the remaining experiments of that very long session
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Commits on Feb 13, 2021

bug fixes
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Commits on Feb 16, 2021

bug fixes + using allen sdk for stimulus table
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committed
Merge branch 'dev' into feature/clustering
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committed
edits
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committed
bug fix
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bug fix
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Commits on Feb 17, 2021

setting mouse history code made much cleaner
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Commits on Feb 22, 2021

multiscope paper; data release sessions included
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committed
Merge branch 'dev' into feature/clustering
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committed

Commits on Mar 5, 2021

svm engagement image decoding
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Merge branch 'dev' into feature/clustering
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committed

Commits on Mar 6, 2021

svm engagement divided trials; pupil; running
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bug fix
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Commits on Mar 9, 2021

svm pupil engagement image selectivity figure codes updated to take data release sessions
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committed
minor
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committed
correlation; control single beam data; debug
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Commits on Mar 25, 2021

svm decoding change vs no change
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committed
bug fix
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committed
svm plots image change vs no change
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Merge branch 'dev' into feature/clustering
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Commits on Mar 26, 2021

correlating svm image change vs no change with behavioral strategy
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Commits on Apr 2, 2021

Merge branch 'dev' into feature/clustering
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committed

Commits on Apr 3, 2021

svm decode hit vs miss
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Commits on Apr 9, 2021

svm: adding the option for balanced trials
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Merge branch 'dev' into feature/clustering
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committed
bug fix
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Commits on Apr 12, 2021

svm: use balanced trials for training and testing datasets
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Merge branch 'dev' into feature/clustering
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minor
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Merge branch 'summary_update' into feature/clustering
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minor
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minor
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Commits on Apr 13, 2021

minor
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bug
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bug fix
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Commits on Apr 14, 2021

svm plots: sumamry across ophys stages
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Commits on Apr 15, 2021

stats code added for anova and tukey; also making stat bars in the plots
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Commits on Apr 16, 2021

edits
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Commits on Apr 17, 2021

weird thing about bool(sys arg); removing it
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bug fix with sys.argv bool str int
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Commits on Apr 24, 2021

svm : engagement added to trials df; cell specimen id added to df
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svm: run the analysis on only engaged times
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Commits on May 4, 2021

behavior strategy correlation with neural activity; scientifica svm analysis
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Commits on May 6, 2021

only engaged in svm bug fixed
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Commits on Jun 9, 2021

scientifica: hit miss decoding
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Commits on Jun 12, 2021

svm scientifica visualization codes updated
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Commits on Jun 15, 2021

svm plotting: reorganizing codes + combining scientifica and mesoscope data
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Commits on Jun 17, 2021

svm plots: pooling scientifica and mesoscope
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Commits on Jun 24, 2021

mesoscope: anova and stats for correlations
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Commits on Jul 7, 2021

svm: baseline vs non baseline decoding incorporated into the svm images code
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slurm codes added
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bugs
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Commits on Jul 8, 2021

slurm params
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test
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slurm debut
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slurm test
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slurm test
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slurm: bug fix
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slurm: bug fix
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slurm bug fix
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slurm bug fix
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slurm fix
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bug fix
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bug
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bug
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bug
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bug
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final slurm!
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bug
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svm gray omit changes to baseline nobaseline
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Commits on Jul 9, 2021

svm runs for the paper
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svm paper figures
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Commits on Jul 12, 2021

svm plots
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Commits on Jul 22, 2021

svm baseline decoding debugged engagement
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Merge branch 'master' into feature/clustering
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experiments table sorting debug
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Commits on Jul 23, 2021

svm next image from omissions debugging ; num classes <8 when using engagement
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Commits on Aug 4, 2021

svm plots area comparison
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Merge branch 'master' into feature/clustering
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Commits on Aug 12, 2021

svm: using matched cells
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bug fixed
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Commits on Aug 18, 2021

svm plotting update
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Merge branch 'master' into feature/clustering
farznaj
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Commits on Sep 23, 2021

Commits on Sep 24, 2021

cell matching for decoding started
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Commits on Sep 30, 2021

Merge branch 'master' into feature/clustering
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Commits on Oct 2, 2021

Commits on Oct 5, 2021

Commits on Oct 8, 2021

stuff
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Commits on Oct 12, 2021

Commits on Oct 14, 2021

Commits on Oct 15, 2021

Commits on Oct 18, 2021

bug
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Commits on Oct 19, 2021

important bug fixed
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Commits on Oct 20, 2021

bugs fixed for mesoscope data related to matched cells
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Commits on Oct 22, 2021

container id and experience level added to svm file; additional edits to plotting based on experience level
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Commits on Oct 29, 2021

important edits; plotting based on experience level; proper svm results pandas table is made
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Commits on Oct 30, 2021

final: svm plotting codes for comparing experience levels for the paper
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Commits on Nov 1, 2021

experience level visualization codes
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Commits on Nov 14, 2021

svm plots; pooled project codes; time course of decoding; interpolation
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Commits on Nov 16, 2021

Commits on Nov 20, 2021

multiscope paper: noise correlation distributions
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Commits on Jan 4, 2022

full population decoding
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Commits on Jan 7, 2022

Commits on Jan 14, 2022

Commits on Feb 19, 2022

codes added to make svm comparison of area and depth plots
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Commits on Feb 22, 2022

Merge branch 'master' into feature/clustering
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Commits on Feb 25, 2022

multiscope paper; reviewer comments; correlation heatmaps on the same scale etc
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Commits on Feb 28, 2022

Commits on Dec 2, 2022

Merge branch 'master' into origin/decoding
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Commits

Commits on Jun 17, 2020

Commits on Jun 19, 2020

Commits on Jun 20, 2020

Commits on Jun 25, 2020

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