Welcome to the SpyKING CIRCUS’s documentation!


The SpyKING CIRCUS is a massively parallel code to perform semi automatic spike sorting on large extra-cellular recordings. Using a smart clustering and a greedy template matching approach, the code can solve the problem of overlapping spikes, and has been tested both for in vitro and in vivo data, from tens of channels to up to 4225 channels. Results are very good, cross-validated on several datasets, and details of the algorithm can be found in the following publication: http://biorxiv.org/content/early/2016/08/04/067843


In 0.5, smart search is now activated by default, and important changes have been done under the hood to refactor the code in order to read/write virtually any file format, as long as a wrapper is provided. Be in touch if you are interested by writing your own wrapper. A “garbage collector” mode has also been added, to help the user to get a qualitative feedback on the performance of the algorithm, estimating the number of missed spikes: spikes left unfitted during the fitting procedure can be collected, grouped by electrode (keep in mind that this is more for a debugging purpose, and those spikes are only an approximation).


The latest version is 0.5, but still in beta. (Latest stable release is 0.4.3) Fixes/improvements can be made here and there based on feedback from users, especially regarding the API to handle various file formats. So please always be sure to regularly update your installation. If you want to be kept updated with fixes, please register to our Google Group: https://groups.google.com/forum/#!forum/spyking-circus-users.