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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 existing file, but rather appends “-01” to the file name. If that filename already exists as well, it will append “-02” instead, and so on. 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. Now we need to 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). For that purpose you might want to do the following steps in any order (potentially even going back and forth):
    • Create combined (phys+behavior) files (implemented in phys_gui)
    • Plot single unit tuning assuming cells are unique in every block (implemented in phys_gui) - This is meant to help assessing if two “units” in the same block might actually be the same (if they have very similar tuning properties)
    • Re-sort PLX file (combining same cells sort codes of same block same channel)
  6. If you have finalized the sorting, create combined (phys+behavior) files (implemented in phys_gui) (yes, once again, now that you have a different amount of cells)
  7. Complete Same cells file
  8. Automatically update the automatic_sorting sheet from the Excel sorting table using phys_gui
  9. Copy the automatic_soting entries to the final_sorting sheet of the Excel sorting table and complete with manual entries.
ephys_pipeline/pipeline_overview.txt · Last modified: 2017/11/23 12:45 by lukas.schneider