Launching the visualization GUIs

You have several options and GUIs to visualize your results, just pick the one you are the most comfortable with!

Matlab GUI

Installing MATLAB

SpyKING CIRUCS will assume that you have a valid installation of MATLAB, and that the matlab command can be found in the system $PATH. For windows user, please have a look to this howto. For unix users (mac or linux), simply add the following line to your .bash_profile or .bashrc file, in your $HOME directory:

export $PATH=$PATH:/PATH_TO_YOUR_MATLAB/bin/matlab

Then relaunch the terminal

Launching the MATLAB GUI

To launch the MATLAB GUI provided with the software, you need of course to have a valid installation of MATLAB, and you should be able to simply do:

>> circus-gui-matlab path/mydata.extension

Note that in a near future, we plan to integrate all the views of the MATLAB GUI into phy

To reload a particular dataset, that have been saved with a special suffix, you just need to do:

>> circus-gui-matlab path/mydata.extension -e suffix

This allows you to load a sorting session that has been saved and not finished. Also, if you want to load the results obtained by the Meta Merging GUI, you need to do:

>> circus-gui-matlab path/mydata.extension -e merged


To launch the phy GUI (pure python based using opengl), you need a valid installation of phy 2.0 and phylib.

Installing phy 2.0

If you want to use the phy GUI to visualize your results, you may need to install phy 2.0. If you have installed SpyKING CIRCUS within a conda environment, first activate it:

>> conda activate circus

Then, once you are in the environment, install phy 2.0:

(circus) >> pip install colorcet pyopengl qtconsole requests traitlets tqdm joblib click mkdocs dask toolz mtscomp
(circus) >> pip install --upgrade
(circus) >> pip install --upgrade

Launching the phy 2.0 GUI

If phy 2.0 is installed, you should be able to simply do:

>> spyking-circus path/mydata.extension -m converting -c N

Followed by:

>> circus-gui-python path/mydata.extension

As you see, first, you need to export the data to the phy format using the converting option (you can use several CPUs with the -c flag if you want to export a lot of Principal Components). This is because as long as phy is still under development, this is not the default output of the algorithm. Depending on your parameters, a prompt will ask you if you want to compute all/some/no Principal Components for the GUI. While it may be interesting if you are familiar with classical clustering and PCs, you should not consider exploring PCs for large datasets.


If you want to export the results that you have processed after the Meta Merging GUI, you just need to specify the extension to choose for the export:

>> spyking-circus path/mydata.extension -m converging -e merged
>> circus-gui-python path/mydata.extension -e merged