Free-ware spike sorting
A David Redish
This page updated 24 January 2014.
Contact A. David Redish (redish AT umn.edu) with questions, bug-reports, etc.
If you would like to be included on an MClust-4.0 email list of bug reports, please send an email to ADR with MClust-4.0-registration in the header. The only messages that will go to this email list will be sent by ADR and will refer to data-level bugs in MClust.
Code and distributions
MClust-4.0 (winzip format)
We recommend that all users begin transitioning to MClust-4.0.
MClust has a completely rebuilt engine that is now compatible with the latest versions of Matlab (2012+). Unfortunately, it is not compatible with earlier versions of Matlab.
NOTE: MClust-4.0 should be considered as a beta release and is now available for external testing.
· Loading Engines
Neuralynx .dat format, tetrodes [included in current distribution]
Neuralynx .dat format, singe electrodes [included in current distribution]
Neuralynx .dat format, stereotrodes
Neuralynx old .tt and .dat formats, tetrodes. Works with old SunOS file formats.
· LoadSE_SON (directory)
CED SON files. (Spike2) Written by Shane Heiney. [Washington University in St Louis]
· LoadTT_XX_Neuralinx (directory)
Neuralinx format, allowing non-32 sample loading. Written by Frank Schaupp [Institut fur Neurobiologie, Berlin]
Axona format. Written by Matthijs van der Meer [University of Edinburgh, Edinburgh UK]
Axona format, allows more than 32 samples. Written by Neil Schmitzer-Torbert [Wabash College, Crawfordsville IN]
· BlackRock Loading Engine available from (http://sourceforge.net/projects/npmk/)
Blackrock Grapevine format. Available from Blackrock Microsystems.
Axona format for 64-bit windows. Thanks to Haagen Waade [NTNU. NO].
(These contain some small data sets. I have made no attempt to find “the best examples”, but they should load in appropriately. They can be used to test loading, cutting, and saving functions.)
· TT-sample.Ntt (Load with LoadTT_NeuralynxNT)
· SE-sample.Nse (Load with LoadSE_NeuralynxNT)
· Original MClust by A. David Redish (ADR, current address, University of Minnesota, Minneapolis MN).
Modifications that have been incorporated into version 3.2 were made by
· Peter Lipa (PL, University of Arizona, Tucson AZ)
· Stephen Cowen (SLC, University of Arizona, Tucson AZ),
· Jadin Jackson (JCJ, University of Minnesota, Minneapolis MN),
· Neil Schmitzer-Torbert (NCST, University of Minnesota, Minneapolis MN),
· Francesco Battaglia (batta, University of Arizona, Tucson AZ).
External components shipped with the current distribution include
· BubbleClust (automated spike-sorter, version 0.8) by Peter Lipa (University of Arizona, Tucson AZ).
· Contact Neuralynx for future versions of BubbleClust.
· KlustaKwik (automated spike-sorter) by (Ken Harris, Rutgers University, Newark NJ).
This version incorporates changes from previous versions and is now compatible with the latest versions of Matlab (2007a +). Unfortunately, it is not compatible with earlier versions of Matlab.
[64-bit .mex64 files for XP64 and Vista64 operating systems. (Thanks to Jadin Jackson for compiling these.)] To use these, add them where the mex32 files are. It is not necessary to replace the .mex32 files with the corresponding .mex64 files. Matlab will use the correct ones.
[.mexmaci files for 64bit Mac operating systems. (Thanks to Martin Vinck for compiling these.)] To use these, add them where the mex32 files are. It is not necessary to replace the .mex32 files with the corresponding .mex64 files. Matlab will use the correct ones.
To use these, add them where the mex32 files are. It is not necessary to replace the .mex32 files with the corresponding .mex64 files. Matlab will use the correct ones.
Neuralynx’s Cheetah 5.X has a deeper bit-depth than earlier versions of Cheetah. To accommodate this bit depth, you need to change the global variable MClust_AverageWaveform_ylim in MClustResetGlobals to 16* its old value.
· MClust-3.4.beta.zip (winzip format)
We recommend using MClust-3.4 for all users of Matlab versions earlier than 2007a.
Jadin Jackson (University of Amsterdam) has developed a new version of MClust 3.4 with multi-step undo and incorporated ICA.
· MClust-3.5 Extras. Extra features and additional components for MClust-3.5.
· A number of extra components are included in various subdirectories under “Extras”. Simply move these from the “Extras” directory to their respective parent directory to use.
18 July 2012
· Balazs Hangya (Cold Spring Harbor)
· Matthijs van der Meer (University of Minnesota)
- RemoveDoubles – removes double-counted spikes. To use, put in the @mccluster directory.
(University of Amsterdam)
- new GeneralizedCutterOptions
[including CloseAllNonEssentialFigs, ShowAllWaveforms, SortClustersByColor]
- new ClusterOptions
[including CutOnBestProjection, FindBestCQProjections]
These extras have not been tested with MClust-3.5.
Recent additions include
· new GeneralizedCutterOptions [including ShowAllAverageWaveforms, ShowAllXCorrs, ViewAllDimensionPairs]
· new Loading Engine (allowing >32 samples from Neuralynx 32-kHz CSCs) from Michael Krause [Baylor College of Medicine, Houston]
· new Loading Engines from Frank Schaupp [Institut fur Neurobiologie, Berlin]
· new Loading Engine from Shane Heiney [Washington University in St. Louis]
· new version of options from Baldwin Goodell [Montana State University]
· Linux-compatible LoadSE and LoadST engines for Neuralynx-compatible data. [Courtesy Josh Jacobs, Brandeis University]
· new GeneralizedCutterOptions
· new features [Courtesy Baldwin Goodell, Montana State University]
· mclustlinux.tgz. Port to Linux. Done by Nathaniel Daw, Carnegie Mellon University. (28 August 2002)
Written by A. David Redish
· PDF format.