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README-ephys.md

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Extracellular electrophysiology processing

Steps for running (manual):

1. Experimenter should complete input.xlsx spreadsheet with relevant information about experiment
2. Electrode measurements e.g. Intan should be provided as separate Excel workbook e.g. electrode_mappings.xlsx but location referenced in 'electrode_recordings' column. (WIP)

Note: You will need input.xlsx for electrophysiology experiments (sample in root directory) for inclusion of raw data

Files

  • ephys_process3.ipynb (Main Notebook for reading and processing ephys files -> reads input.xlsx and electrode_mappings.xlsx; generates NWB output files)
    • For Intan format, uses ConvertIntanToNWB.py and WriteNWB.py
  • nwb_utils.ipynb
    • code to generate electrode_mappings.xlsx file from source files
    • code to validate NWB files after generation