Manual for the Noisy Spike Generator MATLAB Software: version 0.3 Leslie S. Smith and Nhamoinesu Mtetwa Deprtment of Computing Science and Mathematics University of Stirling Stirling FK9 4LA, Scotland, UK contact: lss@cs.stir.ac.uk 1st February 2006 1 Introduction This tool is used to generate noisy spike trains to simulate the kind of signals that an extracellular electrode (such as those on a multi-electrode array) record from a neural culture. This document is the user manual for the software: a separate document describing the analysis underpinning this is in preparation [2] (an early and incomplete version is available [1]. The tool is intended for use in testing spike detection and spike sorting algorithms: it provides a method of generating realistic spike trains for which the “ground truth” is known. It can also be used simply to generate background noise of the sort that might be encountered by an extracellular electrode. The software generates signals from a single electrode. It can allow for • a number of neurons at different distances from the electrode, some generating cor- related spikes, and some generating uncorrelated spikes • the electrode being partially covered by glial cells The signal that the electrode records is a summation of intracellular spikes from many neurons. The signal is transformed by the response function of the electrode and this is the result of the spatiotemporal distribution of the spikes on the spiking surface of the neuron, and of the path that the signal takes from inside the cell to the electrode. The neurons in the culture are divided into target neurons (which are those that one might be hoping to detect and sort), correlated neurons (whose spikes are correlated with one of the target neurons, but which are to be considered as correlated noise), and uncorrelated neurons (which are intended to provide uncorrelated noise). The number of each type can be set either in the program or from the invoking MATLAB command. 1