Comparative_MEA_dataset/Codes/MATLAB spike detection/Main.m

%Written by Andrey Vinogradov, 2021

%ADD THE CODE DIRECTORY TO MATLAB PATH [either manually or]:
%addpath(genpath('your folder'));

[files,path] = uigetfile('*.h5*',  'Select files for analysis','MultiSelect','on');%(filter)
if iscell(files)
    list=cellfun(@(x) [path x], files,'UniformOutput',false);
    list=list';
else
    list={[path files]};
end
%% PARAMETERS
parameters.min_ref_per = 1.5;              %detector dead time (in ms)
parameters.w_pre = 20;                     %number of pre-event data points stored (def. 20)
parameters.w_post = 44;                    %number of post-event data points stored (def. 44)
%for sampling frequency 24000Hz, pre 20 events, post 44 events
%Reference values. Adjusted for actual sampling frequency deeper in the code
% 24000 events/s -> 20/24000, 44/24000 = handles.par.w_post/handles.par.sr
% pre + post ==> amount of points stored per spike

parameters.detection = 'both';             %type of threshold 'both','neg' or 'pos'
parameters.stdmin = 4.5;                   %minimum threshold factor (def. 5) for the operation with SWTTEO 4.5 should be selected
parameters.stdmax = 50;                    %maximum threshold factor. Is used for artefact removal
parameters.interpolation = 'y';            %interpolation for alignment (not in use here as spike storage is not involved)
parameters.int_factor = 2;                 %interpolation factor (interpolation for spike storing is not in use)
parameters.detect_fmin = 200;              %high pass filter for detection (def. 200)
parameters.detect_fmax = 3000;             %low pass filter for detection (def. 3000)
parameters.segments = 1;                   %nr. of segments in which the data is cutted. --> segmentit voisi analysoida rinnakkain?

%setting of the output directory 
csv_directory = uigetdir('title','SELECT YOUR OUTPUT FOLDER');
%% RUN
runrunman = FileRunner(parameters, list(:,1),csv_directory); %constructor method application
[result, runrunman] = runrunman.ReadSpikesFromNextChannel(); %reading the next channel

while ~isempty(result)
        
	clear result; 
    [result, runrunman] = runrunman.ReadSpikesFromNextChannel();
        
end