MClust

Free-ware spike sorting

A David Redish

University of Minnesota

MClust 3.3/3.4b

This page updated 22 October 2007.

Code and distributions

· MClust-3.3.zip (winzip format)

MClust-3.3 is the final, fully-documented, fully-tested version.

· MClust-3.4.beta.zip (winzip format)

We are also releasing MClust-3.4, which includes a host of new capabilities. We have not fully tested MClust-3.4, nor is it fully documented, but because we don’t know when we will be able to complete the documentation, we are releasing MClust-3.4.beta for those who want/need these additional capabilities.

We recommend using MClust-3.4.beta for all users.

NOTE: The new Matlab (R2007a) requires does not use DLLs the same way as previous releases. This means that you will need to recompile the cpp files for the new Matlab. To do this, in Matlab, first run “mex –setup” and then run “mex [fn].cpp” for each fn.cpp file you can find in the MClust distribution.

· MClust-3-JCJ.zip (winzip format)

Jadin Jackson (University of Amsterdam) has developed a new version of MClust 3.4 with multi-step undo and incorporated ICA.

Additional components

· Loading Engines

· LoadSE_NeuralynxNT (C++, DLL)

Neuralynx .dat format, singe electrodes [included in current distribution]

· LoadST_NeuralynxNT (C++, DLL)

Neuralynx .dat format, stereotrodes [included in current distribution]

· LoadTT_NeuralynxNT (C++, DLL)

Neuralynx .dat format, tetrodes [included in current distribution]

· LoadTT_OLD_NeuralynxSUN_NT (C++, DLL)

Neuralynx old .tt and .dat formats, tetrodes. Works with old SunOS file formats.

· LoadSE_SON (zip)

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]

· LoadTT_Axona (C++, DLL)

Axona format. Written by Matthijs van der Meer [University of Edinburgh, Edinburgh UK]

· LoadTT_Axona50 (C++, mexw32)

Axona format, allows more than 32 samples. Written by Neil Schmitzer-Torbert [Wabash College, Crawfordsville IN]

· Extras. Extra features and additional components for MClust-3.3.

Recent additions include

5 July 2007

· new GeneralizedCutterOptions [including ShowAllAverageWaveforms, ShowAllXCorrs, ViewAllDimensionPairs]

29 June 2005

· new Loading Engine (allowing >32 samples from Neuralynx 32-kHz CSCs) from Michael Krause [Baylor College of Medicine, Houston]

25 August 2004

· new Loading Engines from Frank Schaupp [Institut fur Neurobiologie, Berlin]

18 March 2004

· new Loading Engine from Shane Heiney [Washington University in St. Louis]

11 December 2003

· new version of options from Baldwin Goodell [Montana State University]

21 October 2003

· Linux-compatible LoadSE and LoadST engines for Neuralynx-compatible data. [Courtesy Josh Jacobs, Brandeis University]

2 October 2003

· new GeneralizedCutterOptions

· new ClusterOptions – check out the EditWaveforms, DefineOverlap, BringToTop, and CompareMeans options
[Courtesy Baldwin Goodell, Montana State University]

29 September 2003

· pre-compiled mexglx and mexmac files [Courtesy Baldwin Goodell, Montana State University]

· new features [Courtesy Baldwin Goodell, Montana State University]

Documentation

· PDF format.

· FAQ

Sample files

(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)

Credits

Contact A. David Redish with questions, bug-reports, etc.

· 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).

Errata and Updates

· Some people have had trouble installing MClust-3.0. It is important to “add folders with subdirectories” when setting the path. MClust-3.0 includes multiple subdirectories, all of which must be on your path. [13 June 2002]

· Released version 3.01. Fixes include removing “.dat” name assumption, documentation fixes. FD files generated with MClust-3.0 should be regenerated for version 3.01. [20 June 2002]

· Released version 3.02. Fixes include internal naming conventions, an error which confabulated SC1 and SC10. [9 September 2002]

· Released version 3.03. Changed findAlignment to speed it up by factor of 10. [13 September 2002]

· Released version 3.2. Extensive changes made, including ClusterSeparation, Breaking-the-32-sample-barrier, and many other new options. [20 August 2003]

· Released version 3.2.2. Minor bug-fixes made, including renaming to facilitate unix-based compilation.

· Released version 3.3.

· Released version 3.4 beta. Extensive changes.

· Released version 3.4.1 beta. Minor bug-fixes.

· Released version 3.4.2.beta. Minor bug-fixes.