Free-ware spike sorting
A David Redish
This page updated 14 January 2010.
Contact A. David Redish (redish AT umn.edu) with questions, bug-reports, etc.
If you would like to be included on an MClust-3.5 email list of bug
reports, please send an email to ADR with MClust-3.5-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
We recommend using MClust-3.5 for all
users.
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 Mac operating systems. (Thanks to Anoopum Gupta, Matthijs van der Meer, and Kendra Burbank 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.
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.
· MClust-3-JCJ.zip (winzip format)
Jadin
Documentation
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]
Stephen
Cowen (The Neurosciences Institute) has provided an updated stereotrode
loading engine (
· 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 (directory)
CED
SON files. (Spike2) Written by Shane Heiney. [
· 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 [
· LoadTT_Axona50 (C++, mexw32)
Axona format, allows more than 32 samples.
Written by Neil Schmitzer-Torbert [
· 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.
·
Matthijs van der Meer (
- ShowAllXCorrs.
- RemoveDoubles – removes double-counted spikes. To use, put in the @mccluster directory.
·
Jadin
- new GeneralizedCutterOptions
[including CloseAllNonEssentialFigs, ShowAllWaveforms, SortClustersByColor]
- new ClusterOptions
[including CutOnBestProjection, FindBestCQProjections]
· MClust-3.3 extras. Extra features and additional components for MClust-3.3.
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
·
new Loading Engine from Shane Heiney [
·
new version of options from Baldwin Goodell [
·
Linux-compatible LoadSE
and LoadST engines for Neuralynx-compatible
data. [Courtesy Josh Jacobs,
· new GeneralizedCutterOptions
·
new ClusterOptions –
check out the EditWaveforms, DefineOverlap, BringToTop, and CompareMeans options
[Courtesy Baldwin Goodell, Montana State University]
·
pre-compiled mexglx and mexmac files [Courtesy Baldwin Goodell,
·
new features
[Courtesy Baldwin Goodell,
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)
·
Original MClust by A.
David Redish (ADR, current address,
Modifications that have been incorporated into version 3.2 were made by
·
Peter Lipa (PL,
·
Stephen Cowen (SLC,
·
Jadin Jackson (JCJ,
·
Neil Schmitzer-Torbert
(NCST,
·
Francesco Battaglia (batta,
External components shipped with the current distribution include
·
BubbleClust (automated
spike-sorter, version 0.8) by Peter Lipa (
· Contact Neuralynx for future versions of BubbleClust.
·
KlustaKwik (automated
spike-sorter) by (Ken Harris,
· MClust-3.3.zip (winzip format)
·
mclustlinux.tgz. Port to Linux. Done by Nathaniel Daw,
Written by A. David Redish
Documentation
· PDF format.
MClust (v2.0 for Windows 95/98/NT/2000)
MClust (v2.0 raw, can be compiled for unix)