Spike sorting-tutorial

Spike sor t ing
Tut or ial igo Quian Quir oga
Rodr

Problem: detect and separate spikes
corresponding to different neurons

Goals:
• Algorithm for automatic detection and sorting of
spikes.
• Suitable for on-line analysis.
• Improve both detection and sorting in comparison
with previous approaches.
Outline of the method:
I - Spike detection: amplitude threshold.
II - Feature extraction: wavelets.
III - Sorting: Superparamagnetic clustering.

This tutorial will show you how to
do spike sorting using:

 The wave_ clus graphic user
interface.

 The batch files Get_spikes and
Do_clustering.

Getting started…

• Add the directory wave_clus with subfolders in your
matlab path (using the matlab File/Set Path menu)

• Type wave_clus in matlab to call the GUI.

• Choose DataType simulator and load the file
C_Easy1_noise01_short (in the subdir
wave_clus/Sample_data/Simulator) using the Load
button.

Now you are ready to start playing with wave_ clus …
• This is a 10 sec. segment of simulated data.

• First, choose the option plot_average to plot the average spike shapes (+/- 1
std). Then choose to plot the spike features.

• There may be some spikes unassigned in cluster 0. Go back to plot_all and use
the Force button to assign them to any of the clusters. Better?

• Now change the temperature. At t=0 you will get a single cluster, for large t’s
you may get many clusters (if the parameter min_clus allows it).

• Save the results using the Save clusters button. Load the output file
times_C_Easy1_noise01.mat. Cluster membership is saved in the first column
of the variable cluster_class. The second column gives the spike times.

• You can also change the isi histogram plots using the max and step options.

• Finally check the parameters used in the Set_parameters_simulation file in
the wave_clus/Parametes_files (just type ‘open set_parameters_simulation’ in
matlab).

Playing with the spike features…

• Load the file C_Difficult1_noise015
using again the DataType: Simulator.

• Use the Spike features option

You should get something like this…

Seeing the clusters…
• You may, however, get something different cause SPC
is a stochastic clustering method. If you don’t get the
3 clusters, you may have to change the temperature.

• The are 3 different spike shapes, but you don’t see
three clear clusters. That’s because wave_clus plots in
the main window the first 2 wavelet coefficients.

• You can see the rest of the projections by clicking the
Plot all projections button

It would look like this…

Clusters separate clearly
in some projections

Using Principal ComponentAnalysis

• Now do the same using PCA. Open set_parameters_simulation
and select features = ‘pca’ instead of features = ‘wav’ (don’t
forget to set it back to ‘wav’ when you are done!).

• Load again the data C_Difficult1_noise015.

Why PCA does so bad here?
• As you see, there’s now only one single cluster (and for no temperature
you can split it into 3!). You have just replicated the results of Fig. 8 of
the Neural Computation paper (see reference at the end).

• In this dataset the spike shapes are very similar, and their differences
are localized in time. Do to its excellent time-frequency resolution,
wavelets does much better.

• Also, don’t forget that PCA looks for directions of maximum variance,
which are not necessarily the ones offering the best separation
between the clusters. Wavelets combined with the KS test (see paper)
looks for the coefficients with multimodal distribution, which are very
likely the ones offering the best separation between the clusters.

• As a summary, in the Neural Computation paper it is shown for several
different examples of simulated data a better performance of wavelets
in comparison to PCA.

You are now ready for real data!
• You will now load a ~30’ multiunit recording from a human epilepsy
patient. The data was collected at Itzhak Fried’s lab at UCLA.

• Intracranial recordings in these patients (refractory to medication) are
done for clinical reasons in order to evaluate the feasibility of epilepsy
surgery.

• Load the file CSC4 using the DataType: CSC (pre-clustered). Using the
(pre-clustered) option you will load data that has already been
clustered using the batch file Do_clustering_CSC. If you want to start
from scratch use the CSC option.

• Check the settings in the Set_parameters_CSC file. If you have a
Neuralynx system you can already use the CSC and Sc options for your
own data.

• BTW, there should be a few cool publications coming up using these
human data. If you’re interested check
www.vis.caltech.edu/~rodri/publications in the near future or email me.

It should look like this (if you use the Force button)…

Playing with it…

• Again, you can change the temperature, force the
clustering, see the spike features, etc. Remember
that everything is much faster is you use
Plot_average instead of Plot_all.

• You can also zoom into the data using the Tools menu.

• You may also want to fix a given cluster by using the
fix button. This option is useful for choosing clusters
at different temperatures or for not forcing all the
clusters together.

One further example:

• Sometimes clusters appear at different
temperatures
• In the following example we give a step-
by-step example of a clustering
procedure using the fix button

Step 1: Fix cluster 2 at low T Step 3: Check features

Step 2: Change to T2 Step 4: Fix clusters 2 and 3

Step 5: Change to T3 Step 6: Re-check features

Step 7: Push the Force button

This is how the final clustering
looks like!

Note that after forcing the
green cluster is not as clean as
before.

Clustering your own data…
• Most likely you’ll end up using the ASCII DataType option for your data.

• If you have continuous data, it should be stored as a single vector in a
variable data, which is saved in a .mat file. Look for the file test.mat for an
example. This data should be loaded using the ASCII option or the ASCII
(pre-clustered) if you have already clustered it with the Do_clustering
batch file.

• If you have spikes that have already been detected, you should use the
ASCII spikes option. The spikes should be stored in a matrix named spikes
in a .mat file. The file test1_spikes.mat gives an example of the format.

• You can set the optimal parameters for you data in the corresponding
Set_parameters_ascii (or ascii_spikes) file. Most important, don’t forget to
set the sampling rate sr!

• Important note: To save computational time, if you have more than 30000
spikes in your dataset, by default these will be assigned by template
matching with the batch clustering code (this can be changed in the
set_parameters file). With the GUI, they will stay in cluster 0 and they
should be assigned to the other clusters using the Force button. Note that

Using the batch files…

• There are two main batch files: Get_spikes (for spike detection)
and Do_clustering (for spike sorting). Parameters are set in the
first lines.They both go through all the files set in Files.txt.

• Unsupervised results will be saved and printed (either in the
printer or in a file), but can be later changed with the GUI. For
changing results, you have to load the file with the (pre-
clustered) option. The nice thing is that results for all
temperatures are stored, so changing things with the GUI
mainly implies storing a different set of results rather than
doing the clustering again. Note that using the GUI for
clustering (e.g. with the ASCII option) does not store the
clustering results for future uses.

You are now a clustering expert!
• If you want further details on the method, check:
Unsupervised spike sorting with wavelets and superparamagnetic clustering
R. Quian Quiroga, Z. Nadasdy and Y. Ben-Shaul.
Neural Computation 16, 1661-1687; 2004.

• If you want to keep updated on new versions, give me
some comments or feedback on how wave_ clus
works with your data (I would love to hear about it),
etc. please email me at: rodri@vis.caltech.edu

• Good luck and hope it’s useful!

Spike sorting-tutorial

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