Multichannel Systems MC_Rack Manual - Manual (Page 178)

MC_Rack Manual
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You can also use the commercially available program DataAccess Pro from Bruxton
(www.bruxton.com) to open * .mcd files directly and import data streams into several scientific
graphing and analysis programs.
5.3 Extracting Spikes
5.3.1 Spike Sorting
MeaTools and Matlab for data recorded from MEAs
Prof. Dr. Ulrich Egert from the university in Freiburg, Germany, has designed the MEATools
(www.brainworks.uni-freiburg.de) based on Matlab for analyzing MC_Rack data files recorded
from microelectrode arrays (MEAs). MEATools is available for free and has a graphical user
interface. It is not as easy to use as most commercially available programs, of course. It is especially
useful if you are interested in programming Matlab routines yourself. MEATools is a collection of
useful tools for analyzing spikes and field potentials.
With MEATools, you can sort spikes based on identical principal components, estimate the spike
rate based on moving window rate estimation, calculate PSTH and dot displays, and calculate
burst rates and burst positions.
You can sort spikes based on clustering:
 Pair wise projections of the principal components and spike minima vs. each other (calculated
individually from the spikes on each electrode)
 Projections of the spike minimum vs. time
 Scaling factor of the mean spike cutout
You can review the clusters with different colors for spikes from different clusters, and review
spikes colored for their cluster identity as cutouts against time.
MEATools allows to open *.mcd files directly. In addition to Matlab version 5.3 or higher, you will
need the MC_Stream.dll and MCStreamMEX.dll files installed on the computer from which you
want to run the MEATools. All required files except Matlab are delivered with MC_Rack. Please
see the documentation in the MCStreamSupport subfolder of the MC_Rack program folder
for more information. The Common Program Files folder (for example c:\Program Files
(x86)\Common Files\Multi Channel Systems\) contains the MC_Stream.dll; the Matlab
subfolder contains the other files that are needed for using the MEATools.
Offline Sorter for single electrode or tetrode recordings
Offline Sorter is a commercially available program from Plexon (www.plexoninc.com) for sorting
spike waveforms collected either from a single electrode or tetrode. The sorting is based on
a 3-D principal component algorithm. Offline Sorter supports raw data and spike data streams
from *.mcd files.
Tetrode analysis with Spiker
Spiker is a free program with graphical user interface from a research group at the University of
California, San Francisco, USA (http://millerlab.ucsf.edu/Software/Spiker/spiker.html) for viewing
and interactive clustering of tetrode (multielectrode) recordings.
You can load raw data files generated with MC_Rack in a binary file format with Spiker.
Use the MC_DataTool to convert MC_Rack data streams into binary file format.
Spike2 for spike sorting and tetrode analysis
Spike2 is a commercially available spike analysis program with a graphical user interface and
scripting language from Cambridge Electronic Design Limited (www.ced.co.uk).