http://sigwww.cs.tut.fi/TICSP/CellStats/ 


SDC Morphology Toolbox for MATLAB (powerful collection of latest state-of-the-art gray-scale morphological tools that can be applied to image segmentation, non-linear filtering, pattern recognition and image analysis)
http://www.mmorph.com/ 


Image Acquisition Toolbox
http://www.mathworks.com/products/imaq/ 


Halftoning Toolbox for MATLAB
http://www.ece.utexas.edu/~bevans/projects/halftoning/toolbox/index.html 


DIPimage - A Scientific Image Processing Toolbox for MATLAB
http://www.ph.tn.tudelft.nl/DIPlib/dipimage_1.html 


PNM Toolbox
http://home.online.no/~pjacklam/matlab/software/pnm/index.html 


Another 

ICA / KICA and KPCA (Top) 

ICA TU Toolbox
http://mole.imm.dtu.dk/toolbox/menu.html 


MISEP Linear and Nonlinear ICA Toolbox
http://neural.inesc-id.pt/~lba/ica/mitoolbox.html 


Kernel Independant Component Analysis
http://www.cs.berkeley.edu/~fbach/kernel-ica/index.htm 
Matlab: kernel-ica version 1.2 


KPCA- Please check the software section of kernel machines.

Kernel 

Statistical Pattern Recognition Toolbox 
http://cmp.felk.cvut.cz/~xfrancv/stprtool/ 


MATLABArsenal A MATLAB Wrapper for Classification 
http://finalfantasyxi.inf.cs.cmu.edu/tmp/MATLABArsenal.htm 

Markov (Top) 

MapHMMBOX 1.1 - Matlab toolbox for Hidden Markov Modelling using Max. Aposteriori EM 
Prerequisites: Matlab 5.0, Netlab. Last Updated: 18 March 2002.
http://www.robots.ox.ac.uk/~parg/software/maphmmbox_1_1.tar 

HMMBOX 4.1 - Matlab toolbox for Hidden Markov Modelling using Variational Bayes
Prerequisites: Matlab 5.0,Netlab. Last Updated: 15 February 2002..
http://www.robots.ox.ac.uk/~parg/software/hmmbox_3_2.tar 
http://www.robots.ox.ac.uk/~parg/software/hmmbox_4_1.tar 

Markov Decision Process (MDP) Toolbox for Matlab
Kevin Murphy, 1999
http://www.ai.mit.edu/~murphyk/Software/MDP/MDP.zip


Markov Decision Process (MDP) Toolbox v1.0 for MATLAB
http://www.inra.fr/bia/T/MDPtoolbox/ 


Hidden Markov Model (HMM) Toolbox for Matlab
http://www.ai.mit.edu/~murphyk/Software/HMM/hmm.html 


Bayes Net Toolbox for Matlab 
http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html 

Medical (Top) 

EEGLAB Open Source Matlab Toolbox for Physiological Research (formerly ICA/EEG Matlab toolbox)
http://www.sccn.ucsd.edu/~scott/ica.html 

MATLAB Biomedical Signal Processing Toolbox
http://bsp.pdx.edu/Toolbox/ 


Powerful package for neurophysiological data analysis ( Igor Kagan webpage)
http://igoresha.virtualave.net/Matlab/Unitret.html 


EEG / MRI Matlab Toolbox
http://eeg.sourceforge.net/ 


Microarray data analysis toolbox (MDAT): for normalization, adjustment and analysis of gene expression data.
Knowlton N, Dozmorov IM, Centola M. Department of Arthritis and Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA 73104. We introduce a novel Matlab toolbox for microarray data analysis. This toolbox uses normalization based upon a normally distributed background and differential gene expression based on 5 statistical measures. The objects in this toolbox are open source and can be implemented to suit your application. AVAILABILITY: MDAT v1.0 is a Matlab toolbox and requires Matlab to run. MDAT is freely available at:
http://microarray.omrf.org/publications/2004/knowlton/MDAT.zip

MIDI (Top) 

MIDI Toolbox version 1.0 (GNU General Public License)
http://www.jyu.fi/musica/miditoolbox/ 


Misc. (Top) 

MATLAB-The Graphing Tool
http://sprg.ssl.berkeley.edu/~abrecht/matlab.html 


3-D Circuits The Circuit Animation Toolbox for MATLAB
http://engineering.dartmouth.edu/other/3Dcircuits/

SendMail
http://carol.wins.uva.nl/~portegie/matlab/sendmail/ 


Coolplot
http://www.reimeika.ca/marco/matlab/coolplots.html 


MPI (Matlab Parallel Interface) 

Cornell Multitask Toolbox for MATLAB
http://www.tc.cornell.edu/Services/Software/CMTM/ 


Beolab Toolbox for v6.5
Thomas Abrahamsson (Professor, Chalmers University of Technology, Applied Mechanics, G?teborg, Sweden)
http://www.mathworks.nl/matlabcentral/fileexchange/loadFile.do?objectId=1216&objectType=file 


PARMATLAB


Neural Networks (Top) 

SOM Toolbox 
http://www.cis.hut.fi/projects/somtoolbox/ 


Bayes Net Toolbox for Matlab
http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html


NetLab
http://www.ncrg.aston.ac.uk/netlab/ 


Random Neural Networks
http://www.cs.ucf.edu/~ahossam/rnnsimv2/ 
ftp: ftp://ftp.mathworks.com/pub/contrib/v5/nnet/rnnsimv2/ 


NNSYSID Toolbox (tools for neural network based identification of nonlinear dynamic systems)
http://www.iau.dtu.dk/research/control/nnsysid.html 


Oceanography (Top) 

WAFO. Wave Analysis for Fatigue and Oceanography
http://www.maths.lth.se/matstat/wafo/ 

ADCP toolbox for MATLAB (USGS, USA)
Presented at the Hydroacoustics Workshop in Tampa and at ADCP's in Action in San Diego
http://woodshole.er.usgs.gov/operations/stg/pubs/ADCPtools 


SEA-MAT - Matlab Tools for Oceanographic Analysis
A collaborative effort to organize and distribute Matlab tools for the Oceanographic Community
http://sea-mat.whoi.edu/ 


Ocean Toolbox
http://www.mar.dfo-mpo.gc.ca/science/ocean/epsonde/programming.html


EUGENE D. GALLAGHER
(Associate Professor, Environmental, Coastal & Ocean Sciences)
http://www.es.umb.edu/edgwebp.htm


Optimization (Top) 

MODCONS - a MATLAB Toolbox for Multi-Objective Control System Design 
http://www.eee.kcl.ac.uk/mecheng/jfw/modcons.html 

Lazy Learning Package
http://iridia.ulb.ac.be/~lazy/ 


SDPT3 version 3.02 -- a MATLAB software for semidefinite-quadratic-linear programming
http://www.math.nus.edu.sg/~mattohkc/sdpt3.html 


Minimum Enclosing Balls: Matlab Code 
http://www.compgeom.com/meb/ 


SOSTOOLS Sum of Squares Optimization Toolbox for MATLAB User’s guide
http://www.cds.caltech.edu/sostools/sostools.pdf 


PSOt - a Particle Swarm Optimization Toolbox for use with Matlab
By Brian Birge ... A Particle Swarm Optimization Toolbox (PSOt) for use with the Matlab scientific programming environment has been developed. PSO is
introduced briefly and then the use of the toolbox is explained with some examples. A link to downloadable code is provided.


Plot

http://globec.whoi.edu/software/plotting/gbplot/ 


Signal Processing (Top)

Filter Design with Motorola DSP56K
http://www.ee.ryerson.ca:8080/~mzeytin/dfp/index.html 


Change Detection and Adaptive Filtering Toolbox
http://www.sigmoid.se/ 


Signal Processing Toolbox
http://www.mathworks.com/products/signal/ 


ICA TU Toolbox
http://mole.imm.dtu.dk/toolbox/menu.html 

Time-Frequency Toolbox for Matlab
http://crttsn.univ-nantes.fr/~auger/tftb.html


VoiceBox - Speech Processing Toolbox
http://www.ee.ic.ac.uk/hp/staff/dmb/voicebox/voicebox.html 


Least Squared - Support Vector Machines (LS-SVM) 
http://www.esat.kuleuven.ac.be/sista/lssvmlab/ 


WaveLab802 : the Wavelet Toolbox
By David Donoho, Mark Reynold Duncan, Xiaoming Huo, Ofer Levi
http://www-stat.stanford.edu/~wavelab/ 


Time-series Matlab scripts
http://wise-obs.tau.ac.il/~eran/MATLAB/TimeseriesCon.html 


Uvi_Wave Wavelet Toolbox Home Page 
http://www.gts.tsc.uvigo.es/~wavelets/index.html 


Another 

Support Vector Machine (Top) 

MATLAB Support Vector Machine Toolbox
Dr Gavin Cawley
School of Information Systems, University of East Anglia
http://theoval.sys.uea.ac.uk/~gcc/svm/toolbox/ 


LS-SVM - SISTA


SVM toolboxes
http://www.cs.wisc.edu/dmi/svm/ 


LSVM Lagrangian Support Vector Machine
http://www.cs.wisc.edu/dmi/lsvm/ 


Statistics (Top) 

Logistic regression 
http://www.spatial-econometrics.com/ 

SAGA
http://globec.whoi.edu/software/saga/ 

Multi-Parametric Toolbox (MPT) A tool (not only) for multi-parametric optimization.
http://control.ee.ethz.ch/~mpt/ 

ARfit: A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models
http://www.mat.univie.ac.at/~neum/software/arfit/ 

The Dimensional Analysis Toolbox for MATLAB
Home: http://www.sbrs.de/ 
Paper: http://www.isd.uni-stuttgart.de/~brueckner/Papers/similarity2002.pdf 


FATHOM for Matlab 
http://www.rsmas.miami.edu/personal/djones/ 

PLS-toolbox
http://www.eigenvector.com 

Multivariate analysis toolbox (N-way Toolbox - paper)
http://www.models.kvl.dk/source/nwaytoolbox/index.asp 

Classification Toolbox for Matlab
http://tiger.technion.ac.il/~eladyt/classification/index.htm 

Matlab toolbox for Robust Calibration
http://www.wis.kuleuven.ac.be/stat/robust/toolbox.html 

Statistical Parametric Mapping
http://www.fil.ion.ucl.ac.uk/spm/spm2.html 

EVIM: A Software Package for Extreme Value Analysis in Matlab 
by Ramazan Gen?ay, Faruk Selcuk and Abdurrahman Ulugulyagci, 2001.
Manual (pdf file) evim.pdf - Software (zip file) evim.zip 

Time Series Analysis
http://www.dpmi.tu-graz.ac.at/~schloegl/matlab/tsa/ 

Bayes Net Toolbox for Matlab
Written by Kevin Murphy
http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html 
Other: http://www.isp.pitt.edu/information/toolboxes.html 

ARfit: A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models
http://www.gps.caltech.edu/~tapio/arfit/ 


M-Fit
http://www.ill.fr/tas/matlab/doc/mfit4/mfit.html 


Dimensional Analysis Toolbox for Matlab
http://www.sbrs.net/


The NaN-toolbox: A statistic-toolbox for Octave and Matlab?
... handles data with and without MISSING VALUES. 
http://www-dpmi.tu-graz.ac.at/~schloegl/matlab/NaN/ 


Iterative Methods for Optimization: Matlab Codes
http://www4.ncsu.edu/~ctk/matlab_darts.html 


Multiscale Shape Analysis (MSA) Matlab Toolbox 2000
http://www.vision.ime.usp.br/~cesar/projects/multiscale/ 


Multivariate Ecological & Oceanographic Data Analysis (FATHOM)
From David Jones
http://www.rsmas.miami.edu/personal/djones/ 


glmlab (Generalized Linear Models in MATLAB
http://www.sci.usq.edu.au/staff/dunn/glmlab/glmlab.html 

Spacial and Geometric Analysis (SaGA) toolbox 
Interesting audio links with FAQ, VC++, on the topic 
MATLAB Toolboxes