MATLAB® Tools:
Part of the NeuroMAX vision is the sharing of knowledge,
algorithms, and data among researchers, institutions, and
vendors. As part of that vision, we’re pleased to
provide you with information on other potentially relevant
MATLAB tools that may be of use to you in your neuroscience
research.
The sites listed below may provide open source or commercial
packages. Please read the following summaries and consider
visiting the associated web site.
Academic Programs
Chronux:
www.chronux.org
“Chronux is an open-source software package being
developed for the analysis of neural data. It is a collaborative
research effort based at the Mitra Lab in Cold Spring Harbor
Laboratory. Chronux routines may be employed in the analysis
of both point process and continuous data, ranging from
preprocessing, exploratory and confirmatory analysis. In
addition, it also offers several general purpose routines
such as a routine for extracting specified segments from
data, or binning spike time data with bins of a specified
size.”
FIND
http://www.find.bccn.uni-freiburg.de/
FIND (Finding Information in Neural Data) is an open-source
analysis toolbox for multiple-neuron recordings and network
simulations. Currently the FIND-Toolbox accommodates import
of multiple proprietary data formats, based on the Neuroshare
Project. Physiological data from different acquisition systems
and network simulations environments can now be compared
using identical analysis methods. This allows verifying
results across experiments and laboratories as well as direct
comparison of simulation results and electrophysiological
recordings. This is a project of the Bernstein Center for
Computational Neuroscience Freiburg, Germany.
KlustaKwik
http://klustakwik.sourceforge.net
“KlustaKwik is a program for unsupervised classification
of multidimensional continuous data. It arose from a specific
need - automatic sorting of neuronal action potential waveforms
(see KD Harris et al, Journal of Neurophysiology 84:401-414,2000),
but works for any type of data.”
MClust (A.D. Redish)
http://web.ahc.umn.edu/~redish/mclust/
“MClust is a toolbox which enables a user to perform
automated and manual clustering on single-electrode, stereotrode,
and tetrode recordings. It allows manual corrections to
automated clustering results.”
MatOFF
http://dally.nimh.nih.gov/matoff/matoff.html
MatOFF is a general purpose software tool for behavioral
and electrophysiological studies. It is especially suited
for processing neurophysiological data gathered during the
execution of complex behaviors. MatOFF reads NIMH Cortex
files and has translators for Plexon and other file formats.
It produces raster, histogram, and analog data plots using
a very natural mix of interactive commands, a graphical
user interface (GUI), and batch processing. It even supports
MATLAB scripting within the event search engine, for handling
complex behavioral or data issues from within its integrated
environment.
NeuroSys
http://neurosys.cns.montana.edu/
“The NeuroSys Project provides a set of easy to use
software tools for data sharing by the scientific community.
NeuroSys enables researchers to build their own custom designed
data management systems for annotating querying and (password-protected)
data sharing.”
OSort
http://urut.ch/new/serendipity/index.php?/pages/osort.html
OSort is an open source implementation of a MATLAB-based
online spike sorting algorithm. It includes several spike
detection algorithms, example files, documentation and the
original paper.
Spike Train Analysis Toolkit
http://neuroanalysis.org/toolkit/releases/1.0b/index.html
The Spike Train Analysis Toolkit, developed at the Laboratory
of Neuroinformatics at Weill Medical College of Cornell
University, implements several information-theoretic spike
train analysis techniques. This implementation behaves like
a typical MATLAB toolbox, but the underlying computations
are coded in C and optimized for efficiency.
Wave_clus
http://www.vis.caltech.edu/~rodri/Wave_clus/Wave_clus_home.htm
Wave_clus is a fast and unsupervised algorithm for spike
detection and sorting. Although it gives a first unsupervised
solution, this can be further modified according to the
experimenters’ preference (semi-automatic sorting).
Commercial Programs
AD Instruments: Spike Histogram Module
http://www.adinstruments.com/products/software/research/modules/Spike-Histogram/Windows
The Spike Histogram Module discriminates extracellular spikes
of different amplitudes and widths. Data can be easily exported
to NeuroExplorer to obtain auto- and cross correlograms. Output
files can be saved and exported as MATLAB compatible files.
Alpha Omega: Alpha-Sort
http://www.alphaomega-eng.com/pr_site/details_New.asp?pr_id=45
Alpha-Sort is an offline spike sorter. Spikes are projected
on a two dimensional Principal Component space, and are then
represented by their projections on this space. The package
contains programs for sorting spikes, as well as for quality
control of the resulting classification.
Axona: Tint
www.axona.com/products_s_sba_tint.htm
The Tint tetrode-based cluster-cutting program performs
analysis of hippocampal place cell activity and does firing
rate correlation with various behavioral measures. The spikes
are characterized by parameters including peak-to-peak amplitude,
onset latency and amplitude at a user-specified time. Electrode-pair
scatterplots are generated and separated into clusters either
by a hand-drawn polygon or by a k-means clustering algorithm.
Cambridge Electronic Design: Spike2
http://www.ced.co.uk/spk6wglu.htm
CED's Spike2 identifies and sorts single and multi-unit
activity both on-line and off-line. It can mark events using
simple threshold crossings and sort up to 32 channels on-line
with whole wave spike shape template matching. Cluster cutting
of spikes using PCA and cluster on measurements is also
available.”
Cyberkinetics Neurotechnology Systems, Inc.: Cerebus™
www.cyberkineticsinc.com/content/researchproducts/dataacquisitionsystem.jsp
The Automatic on-line spike detection and automatic spike
classification feature allows researchers to start recording
real time sorted data with little to no setup time. Neural
spikes are automatically detected using an envelope detector
while an automatic detection threshold adapts to the amount
of noise in the signal. The detected neural spikes are then
automatically classified using a template matching algorithm
and a combination of clustering algorithms in feature space.
DataWave Technologies: Autosort
www.dwavetech.com/MainFrm.asp?area=zprods%5CzpiAS
“Autosort is a multi-dimensional spike sorting plugin
that can analyze waveforms data both, real-time while data
is being acquired, and post experiment, from file playback.”
Multichannel Systems: MC_Rack
www.multichannelsystems.com/products-mea/product-details/products/233/mc-rack.html
“Combined with the MC_Card hardware, MC_Rack forms
a complete system for reliable acquisition and analysis
of electrophysiological data. Features include a virtual
oscilloscope, a filter, an event detector, a spike sorter,
automatic feedback, sound, and various analysis tools.”
Neuralynx: Cheetah
www.neuralynx.com/SingleProd.asp?ProdID=113
Cheetah can convert Neuralynx binary data files to Matlab,
ASCII text, and Excel formats. Real-time spike and CSC displays,
in addition to online real-time auto clustering of individual
cells, provide the researcher with precise tools for evaluating
the quality of experiment data.
Nex Technologies: NeuroExplorer
www.neuroexplorer.com
NeuroExplorer includes a variety of analysis options, such
as standard histogram and raster analyses, shift predictors
in crosscorrelograms and color markers in perievent rasters,
Joint PSTH, burst analysis and many more analysis options
and functions, and provides direct data link to Matlab and
Excel.
Plexon: OfflineSorter
www.plexoninc.com/products/offlinesorter.html
“OfflineSorter (OFS) speeds up the process of selecting
and classifying action potential waveforms (spikes) collected
from single electrodes or stereotrodes/tetrodes. Spikes
can be displayed as points in either 2D or 3D feature space,
where a variety of manual, semi-automated, or fully automated
clustering techniques can be applied in order to classify
(sort) the spikes. OFS can also perform spike extraction
on continuously-recorded neural data using several different
thresholding methods. Waveform features and statistics can
be easily exported to MATLAB, Excel or text file.”
RUN Technonogies: Datapac
http://www.runtech.com/
Datapac 2K2 is a comprehensive laboratory applications system
for acquiring, processing, and analyzing many kinds of analog
signals. It offers a collection of optional software modules,
including event detection and spike sorting.
Tucker-Davis Technologies: OpenSorter
http://www.tdt.com/software/for_neuro.htm
“OpenSorter offers a number of powerful sorting methods
including Bayesian expectation-maximization, k-means, and
closest-centers algorithms in addition to manual cluster
cutting and waveform selection.”
