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ephys_pipeline:pipeline_overview

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Ephys pipeline overview

Folder structure

  • Y:\Data\TDTtanks contains the Raw data and sorting related files
  • Y:\Data\Monkey_phys contains the behavioral data
  • Y:\Data\Monkey_phys_mat_from_TDT contains recorded data, arranged in the same trial structure as the behavioral data
  • Y:\Data\Monkey_phys_combined_monkeypsych_TDT contains trial structures with combined behavioral and ephys data

Plexon file naming

\\Session_blocks_N.plx are based on online snippets \\Session_realigned_blocks_N.plx are based on realigned online snippets \\Session_from_BB_blocks_N.plx are based on waveclus clustering \\Importantly, when you save a plx file, it never overwrites an exisitng file, but rather appends “-01” to the file name. If that filename already exists as well, it will append “-02” instead. That means, all files with “-NN” affixes are manually saved. Because of that, for all steps after sorting, we use plx files with the “-01” affix.

Waveclus pipeline

  1. Create waveclus pre-clustering files (implemented in phys_gui)
  2. Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, MATLAB 2014+)
    • Preferentially separate spike shapes in difficult cases
  3. Create plxfiles from WC (implemented in phys_gui)
  4. Check and clean PLX file AND TAKE NOTES (single/SNR/stability rating)
  5. Create combined (phys+behavior) files (implemented in phys_gui)
  6. Plot single unit tuning assuming cells are unique in every block (implemented in phys_gui)
    • Optional, this is meant to help assessing if two “units” in the same block are actually the same
  7. Assess which units are the same within and across blocks (based on channel, electrode depths, spike shapes and potentially tuning, carefully check notes for this)
  8. Re-sort PLX file (combining same cells sort codes of same block same channel)
    • Optional for cases where it was not clear if the “units” are the same
  9. Automatically update the automatic_sorting sheet from the Excel sorting table using phys_gui
  10. Copy the automatic_soting entries to the final_sorting sheet of the Excel sorting table and complete with manual entries.
ephys_pipeline/pipeline_overview.1508938885.txt.gz · Last modified: 2022/12/29 07:15 (external edit)