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)

Calculation of CT MTF and NPS using the ACR accreditation phantom by Saul

This code enables measurements of CT MTF and NPS from images of an ACR accreditation phantom. (computed tomography, ct, modulation transfer f...)

SliceBrowser(varargin)

mtfcalc.m

npscalc.m

Imagine by Christian Wuerslin

4D/3D image visualization and evaluation GUI. (3d, evaluation, image analysis)

Imagine App

OptimalColor(iNBins)

fEvalLineFWHM(SData, sSelectionType, hTexts)

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)

Clarke Error Grid Analysis by Edgar Guevara Codina

Clarke EGA quantifies the accuracy of glucose estimates generated by meters as compared to reference (diabetes mellitus, medical, grid error analysis)

clarke.m

iSignal 2.7 by Tom O'Haver

Interactive smoothing, differentiation, peak sharpening and measurement of time-series signals. (signal processing, data import, chemistry)

pY=isignal(DataMatrix,xcenter,xrange,sm,sw,em,dm,rm,s1,s2,s...

Tools for NIfTI and ANALYZE image by Jimmy Shen

Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform (analyze, niftl, nifti)

affine(old_img, old_M, new_elem_size, verbose, bg, method)

bipolar(M, lo, hi, contrast)

bresenham_line3d(P1, P2, precision)

Negative Binomial Regression by Surojit Biswas

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

nbreg( x, y, varargin )

dynplot by Philipp Homan

Draws what is commonly known as 'dynamite plot'. (statistics, medical, bar chart)

dynplot(y,e,varargin)

Compressed Sensing MRI Phantom (v1.1) by David Smith

A realistic phantom for compressed sensing MRI reconstruction. (image processing, mathematics, measurement)

csphantom (n, bandwidth, signalToNoiseRatio, b1scale, img_r...

example

Nonrigid image registration with fractional differential equations by Nathan Cahill

Solves fractional vector Helmholtz equation in 2D and 3D for use in nonrigid image registration (image processing, medical, image registration)

fractionalHelmholtz2DSliding(varargin)

fractionalHelmholtz3DSliding(varargin)

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

MIMO-Diofantine solver by davood shaghaghi

This function solve MIMO-Diofantine equation. (control design, optimization, simulation)

mimodioph(A,B,N)

Simulink Support for Kinect by Takashi Chikamasa

Simulink Support for Kinect is a set of Simulink blocks interfaced with OpenNI and Kinect SDK. (image processing, instrument driver, demo)

checkDeviceBlock(model, maskType)

checkIMAQBlock(model, blk)

corner_detection_viewer(block)

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)

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

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)

Multifractal detrended fluctuation analyses by Espen Ihlen

The multifractal (detrended fluctuation..., statistics, medical)

MFDFA1(signal,scale,q,m,Fig)

MFDFA2(signal,scale,m,Fig)

Matlabcodes.m

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)

Gantry detector tilt correction by Denny Milakara

Transforms CT DICOMs with Gantry tilt angle (ct, dicom, gantry)

gantry2(varargin)

MSKCC CGDS Cancer Genomics Toolbox by Erik Larsson

Functions for retrieving data from the Cancer Genomics Data Server (CGDS) at MSKCC cBio. (biology, genomics, medical)

cgdstutorial

getcancerstudies(cgdsURL, varargin)

getcaselists(cgdsURL, cancerTypeId, varargin)

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

Animated gif generator from images by Héctor Corte

This script is a GUI to easily generate an animated gif from images. Time between images can be set. (image processing, simulation, interpolation)

gifgenerator.m

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...

Edge Drawer by Héctor Corte

This simple script allows you to create edge pictures from an existent image. (data export, gui, image processing)

edges.m

An Efficient Technique for White Blood Cells Nuclei Automatic Segmentation by Mostafa M. A. Mohamed

This code is implementation of an algorithm to segment the nucleus of white blood cells (WBCs) (medical, white blood cells, image processing)

WBC_SegMadhloom.m

WBC_SegProposed.m

Noise-Power Spectrum by Erik Fredenberg

Generate random noise with a specified noise-power spectrum (NPS) and measure the NPS of an image. (image processing, medical, physics)

...

calc_digital_nps(I, n, px, use_window, average_stack)

cart2rad(nps_x, f_x, n, unq)

Compute SNR for MRI parallel images using different technique by Yingying Wang

There are three methods we used here to compute the SNR of MR images: ACR, SoS, and OPT. (image processing, medical)

idl2matlab(typeArray)

load_nii_hdr(fileprefix)

load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_i...

Electrocorticography / intracranial EEG visualizer by Matthew Davidson

This is a tool for plotting iEEG/ECog data on a brain. (ieeg, ecog, visualization)

ft_group_ieeg_elec_plot(varargin)

keeponly_electrodes(elec, wh)

plot_brain(surf_brain, viewpoint, varargin)

Estimate LDL cholesterol by Igor Podlubny

Estimate LDL cholesterol based on measured total cholesterol (TC), HDL, and triglycerides (TG). (blood test, ldl cholesterol, hdl cholesterol)

estimateLDL(TC, HDL, TG, InputUnits)

Image filtering by CNTM

Improved adaptive complex diffusion despeckling filter (NCDF) (signal processing, image processing, speckle)

twodncdf(imgIn, TMAX)

demo.m

Regularized Common Spatial Pattern with Aggregation (R-CSP-A) for EEG Classification by Haiping Lu

The codes implement the Regularized Common Spatial Pattern with Aggregation (R-CSP-A) algorithm. (signal processing, medical, braincomputer interfa...)

FDA.m

W=RegCsp(EEGdata,gnd,genSs,genMs,beta,gamma)

demoR-CSP-Aggr.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

Genome, SNP marker(s) contingency table(s) by Mohammed Sadeq Al-Rawi

Returns the contingency tables for several markers in case control study. (biotech, single nucleotide pol..., snp)

snp_contingency_tables(R, S)

Simulink model for Fetal ECG extraction (HDL Compatible algorithm) by Igal

This is an HDL Coder compatible Fetal ECG extraction algorithm. (biotech, demo, signal processing)

mom_and_fetus.m

FECG_hdl_fix1

Protein Array Tool by Danny Allen

Converts an image of an R&D Systems Proteome Profiler Array into a list of relative protein levels. (image processing, medical, pharmaceutical)

FitProteinArray(ImageType,TemplateFileName, Manual, ImageFi...

FitProteinArrayGUI()

minBoundingBox(X)

Frost's Filter by Debdoot Sheet

Frost's Speckle reduction filter (image processing, medical)

fcnFrostFilter(inputImage,mask)

OrthoView3D by Jered Wells

MATLAB GUI for exploring 3D datasets through a sleek and simple interface (sample dataset included) (3d, data exploration, orthographic)

orthoview3d(varargin)

3D Free Form Image Registration Toolbox (GUI) by Daniel Markel

A toolbox for performing image registrations on 4D RTOG files or any other volumetric image. (image registration, 3d, image)

Crop_image(varargin)

Dcoord(varargin)

Deform(varargin)

InSPIRE1 - ITK Matlab wraps by Rex Cheung

This is a part of Interactive Specialized Prostate Image Registration Ensemble (optimization, medical, simulation)

Normal Tissue Complication Probability by Rex Cheung

To calculate NTCP models for rectal and bladder toxicity based on DVHs (optimization, statistics, medical)

bladderntcp(param)

Graphical User Interface for Solving Ordinary Differential Equations by Soumya Banerjee

A Graphical User Interface for Solving Ordinary Differential Equations (Immune Response Model) (data export, data import, gui)

odecall_eclipse_tcl_jv_local(target,infected,...

odesolver_outline(varargin)

Matlab Monte Carlo Demo on Advanced Statistical Estimation of Variance and Standard Deviation by Amitava Biswas

Matlab Monte Carlo Demo on Advanced Statistical Estimation of Variance and Standard Deviation (aerospace, automotive, biotech)

biswas48.m

First Order Statistics Filter (Sigma Filter / Lee's Filter) by Debdoot Sheet

First order local neighborhood statistics based image denoising filter. (image processing, medical, signal processing)

fcnFirstOrderStatisticsFilter.m

Homogeneous Mask Area Filter by Debdoot Sheet

Filtering using homogeneous mask within area around a pixel used to estimate the expected gray value (image processing, signal processing, medical)

fcnHomogeneousMaskAreaFilter.m

Maximum Homogeneity over a Pixel Neighborhood for Image Filtering by Debdoot Sheet

Image filtering using switched mean filter with most homogeneous gray values in neighborhood. (image processing, signal processing, medical)

fcnMaxHomogeneityOverPixelNeighborhood.m

gm_wm_contrast by Dave

Calculates contrast between gray matter and white matter of mouse SC MRI Image (image processing, pharmaceutical, medical)

gm_wm_contrast.m