Medical Image Processing Toolbox by Alberto Gomez

Classes and functions for N-dimensional medical image processing, inspired by ITK (image processing, data export, data import)

[img info]=read_mhd(filename)

circle3DMesh(c,r,d,varargin)

coneImage(points_axis, points_side, ref_im)

"April, 2011 Image Processing with MATLAB" webinar demo files by Takuya Otani

MATLAB demo files used in the image processing webinar held on April, 2011 in Japan. (image processing, biotech)

BinaryClose.m

BinaryOpen.m

BinaryOpenClose.m

CODIS by Giuseppe Cardillo

Combined DNA Index System: a GUI tool for forensic paternity lawsuit (gui, biotech)

CODIS(varargin)

CODISINCEST(handles,KC)

CODISswap(a,b,c)

SIMULATION OF PULL-IN EFFECT IN MEMS CAPACITOR USING GUI IN MATLAB by piyush kant

near the 2/3rd of total gap between the plates the response of the mems capacitor gets unstable. (mems, capacitor, simulation)

piyush(varargin)

sim1(varargin)

sim2(varargin)

Four parameters logistic regression - There and back again by Giuseppe Cardillo

Fit data points with a four points logistic regression or interpolate data. (statistics, chemistry, pharmaceutical)

L4Pinv(cf,y)

[cf G]=L4P(x,y,varargin)

N-Dimensional Trapezoidal integral by Mohammed Sadeq Al-Rawi

See title. (communications, biotech, image processing)

trapezoidal_rule_nd_integral(x, mat, N)

Negative Binomial Regression by Surojit Biswas

NB2 Negative-Binomial regression. (statistics, mathematics, optimization)

nbreg( x, y, varargin )

TEC-Controller by Mario Tuerschmann

TEC-Controller plug-in - controls your TEC with a temperature accuracy of 0.001 K (tec, pletier, laser)

TecController

TACTICS Toolbox by Raz Shimoni

TACTICS is an interactive platform for customized high content bioimaging analysis. (image processing, data exploration, biotech)

Renin-Angiotensin-System (RAS) model for SimBiology by Sven Mesecke

Provides a SimBiology model implementation of the Renin-Angiotensin-System (simbiology, pkpd, systems biology)

Continuous Stirred Tank Bioreactor (CSTR) SimBiology model by Sven Mesecke

SimBiology project containing a simple CSTR bioreactor model (simbiology, simbiology model, biotech)

Linear regression for multiple category data with different slopes for each by Soumya Banerjee

The function does OLS and RMA regression on data that is categorized into two different categories (communications, optimization, aerospace)

regress_plot_twocategories_allslope

Chronic Lemphocytic Leukemia Cell Segmentation Using Watershed and optimal Thresholding by Emad Mohammed

this work is to segment the cytoplasm and the nucleus of the CLL microscopic blood images (image processing, biotech)

Chronic_Lemphocytic_Leukemia_Cell_Segmentation_Using_Waters...

Similarity classifier with OWA operators by Pasi Luukka

Toolbox presents vector based classification method which uses similarity measures and OWA operators (classification, fuzzy, biotech)

[Classification_accuracy,p1,m1,classes]=simclass(datalearn,...

[Mean_accuracy, Variance,p1,m1,Means,Vars,Maxsf,Minsf]=simo...

calcfit(data, ideals, y)

Helical Swimming Simulator by Bruce

Simulates a rigid rotating helix at low Reynolds number. (simulation, physics, biotech)

BuildMatrixRegStokes3D(x,X0,N,N0,d)

ExpFlagellumFullTubeMatrix(Sep,Fila_Radius,Radius,Length,La...

F_T_D_RSM(R, a, lambda, L)

MATLAB Tools for Scientist by Asawari Samant

Files from the webinar: MATLAB Tools for Scientists- Introduction to Data Analysis and Visualization (curve fitting, biotech, dose response)

Characterization of Dose-Response Behavior

Dose Response Analysis

DoseResponseFit(varargin)

Binary decision tree by Quan Wang

This software implements binary decision tree classifier in Matlab. (image processing, pattern recognition, machine learning)

T=create01Tree(X,label,Depth,Splits,MinNode)

T=get01Tree(k,T,X,label,Depth,Splits,MinNode)

[d c]=index2depth(k)

Triangular mesh conversion from MATLAB to NASTRAN (ASCII) format and vice versa by Sergey Makarov

Four zipped MATLAB scripts supporting export/import of NASTRAN (ASCII) triangular meshes (triangular mesh, data import, modeling)

Linear regression with statistics for multiple category data by Soumya Banerjee

This function does linear regression with statistics for multiple category data (OLS and RMA) (aerospace, automotive, biotech)

regress_plot_twocategories

A GUI for bacterial identification by juntao jia

A GUI for bacterial identification base on PNN and MDS. (biotech, gui, statistics)

annbis.m

3D image stack viewer by boyexex

Current version only accept gray-scale images. Just format your image stack into a 3D array. (image processing, biotech, demo)

Image_stack_viewer( im_stack )

Convert Gromacs v 4.5 trajectory files into MatLab matrix by Evan

Convert Gromacs trajectory files (.trr) into 3D matrix in matlab. (matlab convert conver..., biotech, simulation)

readGmx2Matlab(coordFile, start_frame, end_frame)

trr2matlab( trajFile, varargin )

Spectra gram by Yucheng Wang

well released code for printing spectra gram (biotech)

GPU Implementation for GVF Force Field by Quan Wang

We implement the GVF force field on GeForce GPU using CUDA. (image processing, optimization, signal processing)

info =mha_read_header(filename)

mha_read_volume(info)

Multi-dimensional (N-dimensional) Gaussian and gaussian derivative filters by boyexex

Parameters: number of dimension (D) filter size (fsize) SD of Gaussian (sigma) (image processing, mathematics, signal processing)

NDgaussian(D,fsize,sigma)

NDgaussian_dev(D,fsize,sigma)

sutterMP285 by M. A. Hopcroft

A class for instrument control of a Sutter MP-285 micromanipulator. (instrument driver, instrument control, serial communication)

SutterPosition(varargin)

sutterMP285

Generating correlation matrices based on the boundaries of their coefficients. by Kawee Numpacharoen

Correlation can be generated using uniform random variable distribution within the boundaries. (statistics, simulation, mathematics)

[C,p]=RandomCorr(n,K)

Active geometric shape models by Quan Wang

The active geometric shape model is a novel approach for fitting a geometric shape in images. (shape model, image processing, optimization)

BoundMirrorEnsure(A)

BoundMirrorExpand(A)

BoundMirrorShrink(A)

Clinical Test Performance by Giuseppe Cardillo

The test calculate the performance of a clinical test based on the Bayes theorem (biotech, pharmaceutical, clinical test perform...)

partest(varargin)

Five parameters logistic regression - There and back again by Giuseppe Cardillo

Fit data points with a five points logistic regression or interpolate data. (statistics, chemistry, pharmaceutical)

L5Pinv(cf,y)

[cf G]=L5P(x,y,varargin)

Three parameters logistic regression - There and back again by Giuseppe Cardillo

Fit data points with a three points logistic regression or interpolate data. (statistics, chemistry, pharmaceutical)

L3Pinv(cf,y)

[cf G]=L3P(x,y,varargin)

Unscented Kalman Filter (UKF) modeling of FitzHugh-Nagumo dynamics by Henning Voss

Unscented Kalman Filter (UKF) applied to FitzHugh-Nagumo neuron dynamics. (unscented kalman filt..., fitzhughnagumo, estimation)

FitzHughNagumo()

Physiologically-based Pharmacokinetic (PBPK) model for SimBiology by Sven Mesecke

Provides a PBPK and a Renin-Angiotensin system model for SimBiology (simbiology, simbiology model, pbpk)

calculateParacellularAbsorption(DrugLogP, DrugMolecularWeig...

calculateTissuePartition(...

Thermal Processing - Updated version by Freddy Del Pozo Leon

This code is designed to help in teaching thermal processing of foods, for food engineering students (food engineering, thermal processing, procesamiento termico)

Thermal_Processing.m

[T_center,T_retort,rho_time,k_time,Cp_time,alpha_time,...

[rho,k,Cp,alpha]=choiokos(T,p,f,c,fi,a,W,I)

a fast method of reading data from PDB files by Evan

This file is a blazingly fast method of reading PDB files (biotech, pharmaceutical, protein data bank)

fastPDBRead(readFile)

Image 3D chao of heart for students by Dit Papa Lamine ndao

database image 3D chao heart (image processing, biotech, signal processing)

v=pacemaker1VI1

Fisher’s Exact Test by Michael Boedigheimer

Hypergeometric cumulative distribution (left, right and two-tailed) including permutation testing. (hypergeometric, statistics, biotech)

fexact( varargin )

NDao's Academic Chao Database figure 1 by Dit Papa Lamine ndao

figures of chao 3D for heart (image processing, signal processing, biotech)

v=pacemaker1VINAIK

A Graphical User Interface for Solving Delay Differential Equations and doing Local Search by Soumya Banerjee

A GUI for solving a set of delay differential equations (DDEs) and local search for best solutions (biotech, statistics, data import)

odesolver_outline

...

dde_auto_fit

Extract platelet area fraction from microscope images by Andrew Irish

Threshold microscope images and calculate object area fractions. (medical, image processing, biotech)

processImages(subdir,DEST_INPUTDIR,DEST_OUTPUTDIR,ATHRESH,T...

A_Z_Node_Spikes by Sam Bateman

For a bio-functional cellphone micro-chip. (biotech, communications, control design)

A_Z_Nodes_Version_2.m

dielectrics by mike

caculate the dielectrics of rough surface ,especially the soil (dielectrics, soil, simulation)

[er,ei]=higheps(theta,f,sand,clay,rhob,rhos)

[er,ei]=loweps(theta,f,sand,clay,rhob,rhos)

[er,ei]=myeps(theta,f,sand,clay,rhob,rhos)

Automated Counting of Bacterial Colonies by Daniel Asarnow

A function to automate bacterial colony counting in images of plated agar in a Petri dish. (biotech, image processing)

colony_count(I,radii)

colony_count_demo.m

OP-AMP basic circuits & filters by Sourav Mondal

Adder, Instrument amplifier, High Pass filter & low pass filter and many others (biotech, communications, data export)

Adder

HPF1st

HPF2nd

Pulsed to tonal strength parameter (PTR) by Ramon Miralles

Parameter to dynamically track the pulsed to tonal mean power distribution. (bioacoustic signal pr..., whale sounds, nondestructive testin...)

ptr(x,Nwindow)

ptr2d(x,Nwindow,fs,overlap,tfr_window,decimationfactor)

tfd(x,Nwindow,overlap,Fs)

Fast Null Linear Discriminant Analysis by Alok

This is the fast implementation of Null LDA method. [W,CPU_TIME]=FNLDA(Data,ClassLabel) (linear discriminant a..., null lda, fast nlda)

FNLDA(Data, Class)

PCRefficiency by Giuseppe Cardillo

Set the Efficiency of a RT-PCR to use in the relative quantification of transcripts. (biotech, pharmaceutical, gene)

E=pcreff(ng,cp)

Detecting PSA failure after radiation treatment for prostate cancer by Rex Cheung

This code has been validated. It finds the PSA failures. (statistics, biotech)

PSAforMatlabCentral.m

Monte Carlo Markov Chain for inferring parameters for an Ordinary Differential Equation model by Soumya Banerjee

This function uses a Monte Carlo Markov Chain algorithm to infer parameters for an ODE model (biotech, data export, data import)

mcmc_ode

analyze_mcmc(parallel)

test_gamma()

LDA for high dimension small sample size data by Bilwaj Gaonkar

Linear discriminant analysis when the data dimensionality is high and sample size is much smaller (medical, image analysis, signal processing)

lda_kernelized.m