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ephys_pipeline:excel_table

Sorted neurons excel table

Find/create the Sorted neurons excel table corresponding to your monkey in the following location: C:\Users\username\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xlsx (replace username with your username, Monkey with the monkey's name and Mon with the first three letters of the monkey's name).

There are two main sheets in this excel file:

  • automatic_sorting
  • final_sorting

The idea is, that a large part of the information can be updated automatically (see…), while some information has to be added manually in the final_sorting sheet. For both sheets, each line represents one unit recorded in one block (and run) AND/OR the corresponding LFP site

Automatically created entries

Monkey Session Date Run Block Chan z Unit N_spk Neuron_ID Site_ID Times_same_unit
Lin 1 2010508 3 1 1 15000a15251Lin_20150508_01Lin_20150508_Site_011
Lin 1 2010508 4 2 1 15000a15251Lin_20150508_01Lin_20150508_Site_011
  • Monkey: monkey initials (first 3 letters)
  • Session: A session counter (irrelevant, but helpful for browsing)
  • Date: Date of recording
  • Run: Corresponding behavioral run
  • Block: ephys recording block
  • Chan: electrode number (channel)
  • z: Electrode depth (from guide tube tip) - taken from electrode depth file
  • Unit: sortcode assigned to this cell (a=first,b=second,…)
  • N_spk: Total spike count
  • Neuron_ID: Cell identifier (the same cell can be recorded in several blocks !)
  • Site_ID: LFP site identifier (Based on electrode depth, same site can be recorded in different blocks and at the same time with different units)
  • Times_same_unit: For identifying unique units

Manually added entries

SNR_rank Single_rank Stability_rank Set Target Hemisphere Grid x y
1 1 0 1 dPulleft22.5-58
3 2 1 1 dPulleft22.5-58

The first three entries should be taken from your notes during sorting.

  • SNR_rank: Signal to noise ratio assessment (1 - best SNR to 3 - marginal SNR)
  • Single_rank: Multiunit or single unit (1 - Single unit (SU) to 3 - Multiunit (MU) )
  • Stability_rank: How stable were the features across time (0 - unit appeared or disappeared during the course of the run; 1 - stable)

The other entries typically don't change within a session and can be taken from the handwritten log (notes taken during recording, to be found in Y:\Logs\Phys

  • Set: Dataset, relevant for assigning to specific project (see dataset convention)
  • Target: Area
  • Hemisphere: left/right
  • Grid: grid identifier (diameter.number)
  • x: grid hole coordinate x
  • y: grid hole coordinate y

Electrode travel

Last, but not least, there is another entry which is typically calculated inside the table using different approaches per experimenter: Electrode_travel. Several columns serve the purpose of calculating the electrode travel (from top of the grid).

Other entries ???

Difficult_sorting_or_unstable_ Other_potential_reasons_to_ignore_or_check Runcomplete Usable Comments task
ephys_pipeline/excel_table.txt · Last modified: 2017/10/26 08:03 by lukas.schneider