spk

Ephys spike loading & analysis tools (Matlab, PLDAPS, Plexon, Kilosort...)

• Analysis functions currently coded for somewhat specific set of MT tuning assessments, but should serve as straightforward example for more generalized use

Dependencies

• Loading .PDS data files requires a current version of the PLDAPS (glDraw branch) in the Matlab path. (...without this, custom data classes, like the condMatrix, cannot be loaded properly)

• All you should need in your path for these analyses to work is PLDAPS and this SPK repo

Code walkthrough example

• ./analysis/exampleAnalysis.m contains a [relatively] commented & cleaned-up walkthrough of an ephys experiment analysis

Working example

• For a working version of the code the walkthrough was based on...

  • start with Matlab in a PLDAPS session directory

    • e.g. /Data/<yyyymmdd>/ , containing a standard set of ./eye, ./pds, & ./spk sub-directories

  • execute tt = scanSesh to retrieve info about the available PLDAPS experiment files within that session

    • this should 'just work' (or fail gracefully) for most PLDAPS experiments utilizing a condMatrix design

    • example tt =

      idx      subj           plx              loc         pdsTime            exptName            viewDist    nPasses    nTrials    durMin
      ___    ________    _____________    _____________    ________    _______________________    ________    _______    _______    ______
       1     {'kipp'}    {'20210915x'}    {'L1P3-6500'}    {'1430'}    {'doXzTune_quik1'     }       60         17         163      37.714
       2     {'kipp'}    {'20210915a'}    {'L1P3-7100'}    {'1548'}    {'doRfPos3d_vdistDots'}       60          2          14      1.8908
       3     {'kipp'}    {'20210915a'}    {'L1P3-7100'}    {'1551'}    {'doRfPos3d_vdistDots'}       60          7          66      5.0414
       4     {'kipp'}    {'20210915b'}    {'L1P3-7100'}    {'1602'}    {'do3dTune_dotBall'   }      101         67        1226      110.59
       5     {'kipp'}    {'20210915b'}    {'L1P3-7100'}    {'1754'}    {'doRfPos3d_vdistDots'}       60          1          20      2.8501
       6     {'kipp'}    {'20210915b'}    {'L1P3-7100'}    {'1757'}    {'doRfPos3d_vdistDots'}       60          8         431      28.941

  • any single experiment in a given session can usually be fully specified by it's pdsTime string

    • e.g. '1551'

    • find a file corresponding to an RF position measurement (exptName likely starting with "doRfPos3d...")

      ... pdsTime            exptName          ...
      ... ________    _______________________  ...
      ... {'1551'}    {'doRfPos3d_vdistDots'}  ...

  • run the rfPosAwake3d.m analysis function to generate receptive field [RF] plots & create the corresponding "dv struct" standard output: dv = rfPosAwake3d('1551', [666,1]) (...see help rfPosAwake3d for details)

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Development & Attribution

Unless otherwise stated, all code written & developed by: Thaddeus B. Czuba, 200x-2022 https://visualstimul.us