gin commit from med068pc183

New files: 1
Modified files: 4

Codes/Connectivity Analysis/Connectivity.m

@@ -1,3 +1,28 @@
+%% CorSE Algorithm for Functional Connectivity
+% This algorithm calculates the correlated spectral entropy (CorSE) based functional 
+%connectivity between % two time series. For more information, 
+%<http://journal.frontiersin.org/article/10.3389/fncom.2016.00112/full Kapucu et al.(2016)>. Please cite the paper if you have used or inspired by the method.
+
+%Copyright (c) 2016, Kapucu
+%All rights reserved.
+%Redistribution and use in source and binary forms, with or without
+%modification, are permitted provided that the following conditions are met:
+%* Redistributions of source code must retain the above copyright notice, this
+  %list of conditions and the following disclaimer.
+%* Redistributions in binary form must reproduce the above copyright notice,
+  %this list of conditions and the following disclaimer in the documentation
+  %and/or other materials provided with the distribution
+%THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+%IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+%DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+%FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+%DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+%SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+%CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+%OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+%OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 %Select the .h5 file for yor analysis
 [file,path] = uigetfile('*.h5');
 

Codes/Connectivity Analysis/License.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2016, Kapucu
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Codes/MATLAB spike detection/Main.m

@@ -1,3 +1,5 @@
+%Written by Andrey Vinogradov, 2021
+
 %ADD THE CODE DIRECTORY TO MATLAB PATH [either manually or]:
 %addpath(genpath('your folder'));
 
@@ -42,17 +44,3 @@ while ~isempty(result)
         
 end
 
-%% DATE EXTRACYION. is it needed?
-%fndates = cellfun(@findMEAdate, SelectedFiles, 'UniformOutput', false);
-%fileinfos = cellfun(@dir, SelectedFiles); %, 'UniformOutput', false);
-        
-% if filename is missing date information that file
-% modification date is used as date
-%for r = 1:length(fndates)
-    %if fndates{r} == 0
-        %fndates{r} = str2num(datestr(fileinfos(r).date,'yymmdd'));
-    %end
-%end
-            
-%fileinfos = {fileinfos(:).datenum}';
-%SelectedFiles = [SelectedFiles fndates fileinfos];

Codes/PCA_code/PCA.m

@@ -1,4 +1,4 @@
-
+%PCA analysis script written by Laura Ylä-Outinen
 X1=readtable('PCA_table.xlsx');
 X1(1:36,1)=table({'hPSC_20517_MEA1and2'});
 X2=X1(:,4:end);

README.md

@@ -91,7 +91,9 @@ The implementational details can be found in the original publication.
 
 The directory `Codes\MATLAB spike detection` contains folder `Functions from F. Lieb's SpikeDetection-Toolbox` which embeds functions imported from [SpikeDetection-Toolbox](https://github.com/flieb/SpikeDetection-Toolbox) distributed under GNU General Public License v3.0. 
 
-The directory `Codes` contains folder `meaRtools` with modified version of [meaRtools package](https://github.com/igm-team/meaRtools) distributed under GNU General Public License v3.0. 
+The directory `Codes` contains folder `meaRtools` with modified version of [meaRtools package](https://github.com/igm-team/meaRtools) distributed under GNU General Public License v3.0. Modifications imply user interface, input file reading and selection process and the addition of [LogISI algorithm](https://doi.org/10.1007/s10827-009-0175-1) for burst detection into the package. The LogISI algorithm originally received from its author Valentina Pasquale was modified for our data and the modifications are mentioned in the publication [Kapucu et al., submitted](http://doi.org/to-be-inserted-after-publication). 
+
+The directory `Codes` contains folder `Connectivity Analysis` with [Spectral entropy based neuronal network synchronization analysis : CorSE](https://doi.org/10.3389/fncom.2016.00112) code distributed under the 3-Clause BSD License.
 
 See the `LICENSE.txt` or `LICENSE` files in the corresponding directories for the full license.