gin commit from med068pc183

Modified files: 1

README.md

@@ -87,19 +87,27 @@ Codes directory contains the following folders:
 
 ## Code Usage Notes
 To launch the MATLAB spike detection code, the user needs to open the *Main.m* file and then add the whole folder containing the MATLAB analysis code to the MATLAB path (so that the program is capable of finding the functions that the code requires). Next, by pressing MATLAB’s green “Run” button, the analysis is launched. The selection of the .h5 raw data files for the analysis is implemented via a pop-up window that opens as the user launches the code. One or more files can be selected for analysis. The output folder selection is performed in the same way. The code sequentially analyses the selected files, providing the user with spike .csv files as an output. If the user decides to use different parameters than described in the methods section for spike detection, the parameters to be changed are located in *Main.m* and *amp_detect.m*.
+
 To implement the analyses in meaRtools, the user needs to follow the steps specified below:
+
 i. First, the user needs to open *MEA_analysis_Axion.R* file.
+
 ii. Then, by clicking the “Source” button, the code is launched. The user sees pop-up windows for selecting the code-containing folder, the output folder, the spike .csv files, the noisy electrode file and the expLog file.
+
 iii. The last pop-up window enables the selection of the analyzed MEA type. There are 12- and 48-well MEA plates available, and the user only needs to enter an integer that corresponds to the analyzed plate type.
+
 The folder selection windows sometimes do not appear on top of the RStudio window; then, they are found in the Windows taskbar. If the user wants to avoid the code directory selection step, it is possible to remove the first pop-up window by replacing the first "choose.dir" function with the code directory address.
+
 It should be noted that electrodes that
 * have no detected spikes (are not mentioned in the MATLAB-generated .csv spike files)
 * are listed in the noisy electrode .csv file
 * are eliminated by the minimum-spikes-per-minute criterion
-are not included in the meaRtools analysis.
-Essentially, if for these abovementioned reasons all electrodes in a particular well are cancelled for all DIVs included in the analysis, this well is not displayed in the analysis output files.
+
+are not included in the meaRtools analysis. Essentially, if for these abovementioned reasons all electrodes in a particular well are cancelled for all DIVs included in the analysis, this well is not displayed in the analysis output files.
 There is a possibility of implementing the code in segments by performing segment selection and pressing the “Run” button.
+
 The PCA and connectivity analysis MATLAB code packages are delivered in their corresponding folders. To run the PCA code, the user needs to open the *PCA.m* code in the "PCA" folder and add the whole folder to the MATLAB path. The folder contains a table with preselected activity features of the cell populations obtained during the provided analysis path. The next step is to click the "Run" button to launch PCA.
+
 To launch the connectivity analysis, the user needs to open the *Connectivity.m* file in the "Connectivity analysis" folder and add this folder to the MATLAB path. After clicking the "Run" button, the pop-up window for .h5 file selection appears. After selecting the desired file, a new pop-up window for MEA well selection appears. The user needs to take into account the list of excluded wells, which are automatically displayed in the command window after the file selection, and avoid selecting them. For the connectivity analysis, the threshold value for connectivity strength can be changed in the script *cross_selection_correlated_channels.m*. More information on the CorSE and analysis guidelines can be found at https://se.mathworks.com/matlabcentral/fileexchange/59626-spectral-entropy-based-neuronal-network-synchronization-analysis-corse.