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OptogeneticInterface #16

Merged
merged 21 commits into from
Apr 23, 2024
Merged

OptogeneticInterface #16

merged 21 commits into from
Apr 23, 2024

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pauladkisson
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@pauladkisson pauladkisson commented Apr 9, 2024 •
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Fixes #8

  • create_stimulation_timeseries from onset times and stim parameters
  • DMS Excitatory example session
  • DLS Excitatory example session
  • DMS Inhibitory example session
  • Ask Lerner Lab for missing data/metadata
  • Iterate through all Opto sessions in convert_dataset script

See Gdrive for example sessions.

@pauladkisson
optogeneticinterface initial setup
db8af88
@pauladkisson
added optogenetic interface and example session
2af7911
@pauladkisson
added comment about optogenetic treatment
76024aa
@pauladkisson
added example sessions for DMS-Excitatory and DLS-Excitatory
617cc47
@pauladkisson
added compression
25eabed
@pauladkisson
refactored fp conversion section into fp_to_nwb()
04a7b35
@pauladkisson
opto_to_nwb initial setup
1ecdc86
@pauladkisson
added missing msn
d4cdbab
@pauladkisson
added support for both left/right stim
d2e1f7f
@pauladkisson
fixed subject ids for aberrant sessions
f7fb4c9
@pauladkisson
added question about dls-excitatory
a292a8f
@pauladkisson
added support for csv sessions in example session
82a4c2f
@pauladkisson
added support for nested medpc files
311197a
@pauladkisson
fixed indentation bug
4a7c6c2
@pauladkisson
added support for sessions without stim
b847055
@pauladkisson
added support for csv sessions in convert_dataset
58b34bf
@pauladkisson
fixed pandas dtype warning
ea4a3ba
@pauladkisson
fixed DtypeConversionWarning
44fb51a
@pauladkisson
fixed pandas dtype warning for convert_dataset
5270d66
@pauladkisson
added support for start dates and times from csvs
89da646
@pauladkisson
added docstrings
6026df0
@pauladkisson pauladkisson marked this pull request as ready for review April 16, 2024 23:56
@alessandratrapani
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In the file linked in the description I can't see any optogen data. I think that stub it's just for behavior. Can you share a version with optogen too?

alessandratrapani
alessandratrapani reviewed Apr 19, 2024
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@alessandratrapani alessandratrapani left a comment

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Very well done! I'll wait a example .nwb before approving

@pauladkisson
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Whoops, sorry about that. Should be fixed now.

@pauladkisson pauladkisson mentioned this pull request Apr 22, 2024
Merged
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@pauladkisson pauladkisson merged commit ebb02e4 into main Apr 23, 2024
@pauladkisson pauladkisson deleted the optogenetics branch April 23, 2024 08:27
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@alessandratrapani alessandratrapani alessandratrapani approved these changes

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Optogenetic Interface
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@pauladkisson @alessandratrapani