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default.m
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% preferences file for spikesort
% spikesort has many preferences, and, instead of wasting time building more and more UI to handle them, all preferences are in this text file (like in Sublime Text)
% this is meant to be read by readPref
%
% created by Srinivas Gorur-Shandilya at 4:52 , 16 September 2015. Contact me at http://srinivas.gs/contact/
%
% This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
% To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.
%% ~~~~~~~~~~~~~~~~~ DATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
deltat = 1e-4; % what is the time step of the data?
ephys_channel_name = 'voltage'; % what is the name of the variable that contains the ephys recording in your data?
stimulus_channel_name = 'PID'; % what is the name of the variable that contains the stimulus recording in your data?
%% ~~~~~~~~~~~~~~~~~ GENERAL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
useFastBandPass = false; % use a fast, FFT-based bandPass?
%% ~~~~~~~~~~~~~~~~~ DISPLAY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
putative_spike_colour = 'm';
embedded_spike_colour = 'g';
A_spike_colour = 'r';
B_spike_colour = 'b';
% display preferences
marker_size = 5; % how big the spike indicators are
show_r2 = false; % show r2 in firing rate plot
fs = 14; % UI font size
fw = 'bold'; % UI font weight
plot_control = true; % should spikesort plot the control signals instead of the stimulus?
% UI
smart_scroll = true; % intelligently scroll so we keep # visible spikes constant
% context width: window around the spike to show when clicked on in a reduced representation
context_width = .2; % seconds.
% density peaks automatic cluster visualization
show_dp_clusters = true;
%% ~~~~~~~~~~~~~~~~~ LFP, RASTER AND FIRING RATE PLOTS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
show_individual_trials_stimulus = false;
show_individual_trials_LFP = false;
show_individual_trials_firing_rate = false;
% firing rate estimation
show_firing_rate_r2 = false; % show r-square of firing rates?
firing_rate_dt = 1e-2; % time step for firing rate estimation
firing_rate_window_size = 3e-2; % window size for firing rate convolution
%% ~~~~~~~~~~~~~~~~~ SPIKE DETECTION AND RESOLUTION ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
% spike detection
t_before = 20; % should be an integer, in units of data samples
t_after = 25; % should be an integer, in units of data samples
minimum_peak_prominence = 'auto'; % minimum peak prominence for peak detection. you can use 'auto' or you can also specify a scalar value
minimum_peak_width = 1;
minimum_peak_distance = 1; % how separated should the peaks be?
V_cutoff = -1; % ignore peaks beyond this limit
band_pass = [5 .5]; % in ms. fluctuations longer than the first element are ignored, and fluctuations shorter than the second element are averaged across.
invert_V = false; % sometimes, it is easier to find spikes if you invert V
% spike resolution
remove_doublets = true; % resolve doublet peaks, which are very likely AB or BA, not AA or BB
doublet_distance = 40; % how far out should you look for doublets? in units of timestep
% artifact removal
remove_artifacts = 'off'; % 'on' or 'off'.
template_width = 100;
template_amount = 0;
use_off_template = false;
use_on_template = false;
%% ~~~~~~~~~~~~~~~~~ tSNE parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
no_dims = 2;
init_dims = 10;
perplexity = 60;
theta = .5;
max_iter = 400;
multicore_tsne_path = '~/anaconda3/bin'; % change this to the path where MultiCoreTSNE is installed