Tutorial Synthetic Data

Tutorial Part I

1. Download Sample Data

In this part of the tutorial, we will work with synthetic (simulated) data. We will work with the file

http://bioweb.me/CPGJNM2012-dataset/simulation_5.mat.

Download the file.

For the curious

The simulated data was produced by Carlos Pedreira and colleagues. Details can be found in:

Pedreira, C., Martinez, J., Ison, M. J., Quian Quiroga, R.: "How many neurons can we see with current spike sorting algorithms?" Journal of Neuroscience Methods 211 (1), 2012. doi:10.1016/j.jneumeth.2012.07.010.

2. Extracting Spikes

After downloading the simulated data, move the command prompt to the folder where you stored it and enter

css-extract --matfile simulation_5.mat.

There is now a folder simulation_5, containing one file data_simulation_5.h5.

3. Clustering Spikes

In this tutorial we try to keep things simple. So just enter

css-simple-clustering --datafile simulation_5/data_simulation_5.h5.

After a few seconds, the folder simulation_5 contains the sorted data.

4. Checking Results

Now we would like to see the output of the clustering procedure. There are two main ways for visualization.

4.1 Using overview plots

Enter

css-plot-sorted --label sort_pos_simple.

There is now a folder overview, containing just one plot:

The red numbers 1. through 4. point at a few problems with the clustering that we are going to solve soon.

4.2 Using the graphical user interface

Enter css-gui and click on File, Open. You will see a list containing just one file, our Simulation 5. Click on OK.

You will see this (or a similar) screen:

Go through the individual cluster groups by using the pull down menu. The plots on the right hand side update automatically. In our screenshot you can see that the unit displayed is "under-clustered": it should be split apart further. We will solve this problem later in this tutorial.

Now, click on the "All Groups" tab. You will see this (or a similar) screen:

Here you see an overview of all cluster groups contained in Simulation 5. In some cases, clusters are grouped together in the wrong way. To solve this:

• First create a new group by clicking Actions, New Group.
• Then click on one of the clusters you would like to move to the new group (red 1. in the screenshot)
• The last step is to click into the new, empty group (red 2. in the screenshot).

You can save your modification by clicking File, Save.