02 Using the Scripts

Installing Dependency

MLspike Toolbox

1. Download the toolbox at here

2. Open MATLAB. Go to "Home" -> "Set Path"

3. Add the two folders (brick and spikes) to the path. Do not include sub-folders.

Bio-Format Toolbox

1. Download the toolbox bfmatlab.zip here

2. Follow the installation instructions here

3. If the data set is big, you may need to increase the Java Heap Memory

Additional scripts

1. Download the scripts from Scripts

Running the Script

1. Open the script multi_cell_activity_detection_pipeline.m.

2. Change the file path in the session "Defining parameters".

3. Use Run and Advance to run the sections one by one. It is recommended to check if the default parameters apply to your data. For details of parameters used in each section, refer to 03 Data Processing.

4. You may use the Run button if you are satisfied with the parameters.

Citations

Cite this paper for the spike train deconvolution algorithm MLspike.

Cite this paper for using the Bio-Format toolbox.