Tetrodes sorting

Default parameters for JRCLUST are optimized for high-density silicon probes. For tetrodes recordings, I recommend following settings based on the simulated tetrodes ground-truth dataset provided by Jeremy Magland.

Parameter file

vcFilter = 'bandpass'; % Use bandpass filter instead of differentiator filter
freqLim = [300, 3000]; % Bandpass frequency range
maxSite=1.5;           % Total number of sites per spike event is 1+2*maxSite. For tetrode, 1+2*1.5=4
nSites_ref = 0;        % no reference sites available for tetrodes
vcSpkRef = 'none';     % turn off local CAR subtraction
vcCommonRef = 'none';  % common reference mode {'none', 'mean', 'median', 'whiten'}
nPcPerChan = 2;        % Number of PC per chan. Default is 1 but tetrodes may need more temporal features due to limited number of channels per event group.
maxWavCor = .99;         % Disable merging based on waveform similarity, four channels are too little to do this.
fft_clean = 10;        % (Optional) if there is narrow-band noise in your recording (run `jrc preview` to check the power spectrum).

Probe file

• For a recording containing two tetrodes, where tetrode 1 contains channels 1..4 and tetrode 2 contains channels 5..8
• see /prb/tetrodes.prb in JRCLUST folder for an example configuration for four tetrodes.

channels = 1:8;                      % 8 channels mapped to sites
shanks = [1 1 1 1, 2 2 2 2];         % group channels by tetrode group (treated as separate shanks)
geometry = [0 25 0 25 0 25 0 25; 0 0 25 25 100 100 125 125]';   % (8 x 2 matrix, fist col.: x pos (um), second col.: y pos (um)

pad = [12 12];  % site pad dimension for visualization (w x h (um))
um_per_pix = 25;   % grid spacing (for visualization)