PhysioNet - Research resource for complex physioloical signals

PhysioNet offers free access via the web to large collections of recorded physiologic signals and related open-source software.

The PhysioNet Resource, intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals, has three closely interdependent components:

PHYSIOBANK

PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. These collections include data from a wide range of studies, as developed and contributed by members of the research community. To begin an exploration of PhysioBank, start here.

PHYSIOTOOLKIT

PhysioToolkit is a large and growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of many of the research projects that contribute software to PhysioToolkit is the extraction of "hidden" information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. All PhysioToolkit software is available in source form under the GNU General Public License (GPL). To learn more about the contents of PhysioToolkit, begin here.

PHYSIONET

PhysioNet is not only the name of the Resource, but also of its web site, physionet.org. The PhysioNet web site was established by the Resource as its mechanism for free and open dissemination and exchange of recorded biomedical signals and open-source software for analyzing them, by providing facilities for cooperative analysis of data and evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software, the PhysioNet web site offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with the annual Computers in Cardiology conference, PhysioNet hosts a series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet.

FREE MATLAB TUTORIAL CD

MATLAB serves as the foundation for all MathWorks products. It includes a programming language and tools for algorithm development, data analysis, data visualization, and numeric computation.

This CD consists of :

Introduction to MATLAB
Data Analysis with MATLAB for Excel® Users
Algorithm Development with MATLAB for C/C++ Products
Introduction to Statistics with MATLAB Products
Introduction to Optimization with MATLAB Products
Application Deployment with MATLAB
MATLAB for Signal Processing
Image Processing Using MATLAB
Data Acquisition with MATLAB Products
Using MATLAB to Develop Financial Products
Introduction to MATLAB for Life Scientists

Click here to get free Matlab tutorial CD .

FREE MICROSOFT SOFTWARES FOR STUDENTS

Microsoft Dream spark offers free microsoft softwares for current university or high school students worldwide.

List of Softwares :

Microsoft Visual Studio 2010 Ultimate

Microsoft Visual Studio 2008 Professional Edition

Microsoft SQL Server 2008 Developer

Windows server 2008 R2 Standard

Windows server 2008 Standard

Windows server 2003

Microsoft Expression Studio 3

Xna Game Studio 3.1

Microsoft Robotics Developer Studio 2008 R2

Microsoft SQL Server Express

Microsoft Visual Studio 2005 Professional Edition

Microsoft Visual PC


Click above links , sing in, verify your student status and download the free softwares

MATLAB TECHNICAL KIT

Click here to download the technical kit of matlab :

MATLAB & Simulink Student Version fact sheet 
MathWorks Product Overview 
MATLAB data sheet
MATLAB and Simulink in the World: Academia
Simulink data sheet
Control System Toolbox data sheet
Signal Processing Toolbox data sheet
Signal Processing Blockset data sheet
Statistics Toolbox data sheet
Optimization Toolbox data sheet
Image Processing Toolbox data sheet
Symbolic Math Toolbox data sheet

Getting Started with MATLAB
MATLAB notes

Getting Started with Simulink
Simulink Tutorial 

MATLAB IN EDUCATIONAL INSTITUTIONS

The MATLAB and Simulink product families are fundamental computational tools at the world's educational institutions. Adopted by more than 3500 universities and colleges, MathWorks products accelerate the pace of learning, teaching, and research in engineering and science. MathWorks products also help prepare students for careers in industry, where the tools are widely used for research and development.

Click here to know how matlab is used in academic institutions.

Matlab Program - Calculating Beat Rate of Heart Using Discrete Wavelet Transform

%Calculating Beat Rate of heart Using Discrete Wavelet Transform
% ECGDATA is the input ecg data file
clear;close all;clc;
load ECGDATA

%Eliminate Baseline Drift
s1=ECG_1;
s2=smooth(s1,150);
ecgsmooth=s1-s2;

%Apply Wavelet Transform
[C,L]=wavedec(ecgsmooth,8,'db4');
[d1,d2,d3,d4,d5,d6,d7,d8]=detcoef(C,L,[1,2,3,4,5,6,7,8]);

%Denoise
[thr,sorh,keepapp]=ddencmp('den','wv',ecgsmooth);
cleanecg=wdencmp('gbl',C,L,'db4',8,thr,sorh,keepapp);

%Thresholding
max_value=max(cleanecg);
mean_value=mean(cleanecg);
threshold=(max_value-mean_value)/2;

%R detection
a5=appcoef(C,L,'db4',5);
C1=[a5;d5;d4;d3];
L1=[length(a5);length(d5);length(d4);length(d3);length(cleanecg)];
R_detect_signal=waverec(C1,L1,'db4');
R_detect_squared=R_detect_signal.^2;

%Beat Rate Extraction
for a=1:length(R_detect_squared)
  if R_detect_squared(a)>threshold
  R_detect_new(a)=R_detect_squared(a);
  else
  R_detect_new(a)=0;
  end
end
mean_R_detect=5*mean(R_detect_new);
for q=1:length( R_detect_new)-1
  if R_detect_new(q)< mean_R_detect
  R_detect_new(q)=0;
  end

end

d=0;
for b=1:length( R_detect_new)-1
  if ( R_detect_new(b)==0) & ( R_detect_new(b+1)~=0)
  d=d+1;
  indext(d)= b+1;
  end
end
fs_R_detect=length(R_detect_new)/20;
time=indext.*1/fs_R_detect;
ind=0;
for z=1:length(time)-1
  ind=ind+1;
  time_diff(ind)=time(z+1)-time(z);
end
av_time=mean(time_diff);
Square_Number=av_time/.2;
beat_Rate=300/Square_Number;
high=max(R_detect_new);

% Plot the Orginal Signal and Eliminating Baseline Drift signal
% Plot Denoised signal & R Detected Signal
subplot(4,1,1);plot(s1);title('ORIGINAL SIGNAL');
subplot(4,1,2);plot(s1-s2);title('BASELINE DRIFT ELIMINATION');
subplot(4,1,3);plot(cleanecg);title('MAIN SIGNAL(DENOISED ECG)');
subplot(4,1,4);plot(R_detect_new);title('R DETECTED SIGNAL');
text(length(R_detect_new)/2,high,['BEAT RATE = ',num2str(fix(beat_Rate))],'EdgeColor','Blue');

IDL (Interactive Data Language) in Medical Imaging

IDL is the software platform chosen by medical imaging professionals who need to analyze, display, process, interpret and share medical imaging data. IDL's powerful visualization and analysis capabilities help you understand medical images from virtually any modality and integrate custom tools across the health care enterprise.

Clinical Medical Imaging Applications

Getting accurate and useful information from your images in a clinical setting is a priority. In both diagnostic and treatment applications IDL gives you the flexible data analysis and visualization tools you need get answers from your images. IDL offers interoperability with all types of data and a variety of leading medical imaging workstations, as well as a compliment of DICOM options to make IDL a contiguous and integral part of the clinical medical imaging workflow.

Research Medical Imaging Applications 
 
Medical imaging researchers worldwide depend on IDL to analyze medical imaging data and to develop new algorithms to aid in their research. IDL is an intrinsic part of the discovery process, piloting numerous projects from prototype to clinical application. IDL users can leverage the experience of a vast global user community, sharing an extensive library of IDL algorithms and expertise. IDL's cross-platform functionality, distribution options and DICOM functionality enable medical imaging application collaboration with colleagues across the hall or even across the globe.

Commercial Application Development 
 
IDL is the development platform of choice for many of the leading medical imaging toolkit providers. IDL gives application developers the tools to create customized applications, for both standalone environments and medical imaging workstations. The use of IDL for commercial applications continues to grow with the expansion of IDL's DICOM options, multiple distribution options and the ongoing advances in IDL bridging technologies such as Java, and ActiveX bridges.

About IDL 

IDL is the ideal, timesaving solution for data analysis, data visualization, and software application development. From “quick-look” analysis and display to commercial programming projects, IDL combines the technology and tools you need with a modern, extensible environment.

IDL requires less code and programming expertise to produce dynamic visualizations and analyses, or to develop powerful software applications with user-friendly interfaces. And, since the IDL software development environment, the IDL Workbench is based on the popular, open-source Eclipse framework, it is truly a cross-platform solution.

Professionals like you across industries rely on IDL to access, analyze, visualize, develop, integrate, and share information from data.

Click here to download IDL .


 

LIST OF BIOSIGNAL PROCESSING SOFTWARES

BioSig - library for biomedical signal processing featuring, for example, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on.

ecg2png - Program designed to convert scanned 12-lead electrocardiograms into PNG format

LIST OF MEDICAL IMAGING SOFTWARES

3D Slicer - Medical Visualization and Processing Environment for Research
Amide - Tool for viewing, analyzing, and registering volumetric medical imaging data sets, actively being developed
BioImageXD - Software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources
BrainStorm - An electro/magnetoencephalography (EEG/MEG) data processing and vizualisation toolbox.
BrainVisa - A brain imaging package including data processing and visualization capabilities, such as T1-based gyrus segmentation, diffusion-based fibertracking, PET, MEG, EEG and more.
CDMedic PACS
ClearCanvas Workstation - An open source DICOM workstation and application framework for developing medical imaging applications.
CTSIM - Computed Tomography Simulator
DCM4CHE - Open Source Clinical Image and Object Management written in java
DCMTK - A collection of libraries and applications implementing large parts the DICOM standard
DeVIDE - The open source (BSD-style license) and cross-platform (Windows, Linux) Delft Visualization and Image processing Development Environment, a visual programming system focused on medical visualization and image processing. DeVIDE incorporates VTK, ITK, numpy, matplotlib, DCMTK and GDCM. Latest features include a visual DICOM browser.
dicom4j - An open source DICOM Java framework.
Dicom4j-apps - Free and open-sources DICOM applications in Java.
DICOM Router - A variety of DICOM related utilities
DICOM Validation Tool (DVT) - A software utility and a set of .NET components that will assist in testing the medical / healthcare protocol DICOM. DVT provides you the methods to transfer and validate DICOM objects.
Drishti - A volumetric visualisation package for viewing Computer Tomography data. Able to import DICOM image stacks.
ecg2png - Program designed to convert scanned 12-lead electrocardiograms into PNG format
Endrov - Image and data viewer and editor
Eviewbox - Java medical imaging software
GDCM Grassroots DiCoM - A C++ library for DICOM medical files. It is automatically wrapped to python/C#/Java (using swig). It supports RAW,JPEG (lossy/lossless), J2K,JPEG-LS,RLE and deflated. It also comes with DICOM Part 3,6 & 7 of the standard as XML files.
Imlib3d - C++ library for 3D (volumetric) image processing
ITK - Segmentation and Registration Toolkit
ITK-SNAP - Interactive software for 3D image navigation, annotation and automatic segmentation
kradview - Free (GPL) DICOM viewer, for Linux and FreeBSD.
METK - An open source toolkit to visualize and explore medical datasets.
miniwebpacs - Storage, control and recovery of medical images and information in healthcare providers of small and medium capacity. Such system is based on the DICOM standard and in the actual WEB technologies.
MITK - Medical Imaging Interaction Toolkit
NIRFAST - An open source FEM based software package designed for modeling Near Infrared Frequency domain light transport in tissue.
O3-RWS - The Radiology Workstation of the Open Three ( O3 ) Consortium. According to the IHE definitions, O3-RWS is an Open Source, DICOM based, Internationalized, Modular and Portable Image Display actor plus the integration of several other IHE actors.
OsiriX - 3D DICOM Medical Viewer for Mac OS X. Complete DICOM Viewer with DICOM network support
Ogles - A three-dimensional volume and slice data visualization tool
Opensource PACS - Wet Read system includes: image order, image reconciler, radiologist workstation (DICOM viewer), DICOM structured reporting, web-based summary of patient diagnosis.
ParaView - Large Scale Visualization tool
PhP Nuke healthcare - X-Ray and Register modules for storing patient data with pictures. System is DICOM compatible
Tempo(Topographic Eeg Mapping PrOgram) - Open source software for 3D visualization of brain electrical activity
Virtual PACS - Allows radiologists to use a DICOM workstation to access multiple DICOM repositories as a single federated virtualized PACS. The DICOM repositories are exposed on caGrid and can include PACS, image archives such as National Cancer Imaging Archive or other DICOM data warehouses.
Voreen - Volume Rendering Engine - A library providing essential functionality for visually exploring volume data sets. Voreen supports most relevant data formats as for instance DICOM and is currently used in medical visualization as well as for visualizing electron microscopy data.
VTK - Visualization Toolkit
Xebra - Medical imaging software

LIST OF BIOMEDICAL SOFTWARES

1.) Crystallography and NMR softwares

CNS - Crystallography & NMR System
CCP4 (macromolecular crystallography program suite)
DYANA - Program for NMR structure calculation that provides all functionality of its predecessor, DIANA and many new features.
DINOSAUR - Program for structure refinement using direct NOE restraints.
IRMA2 - IRMA procedure calculates distances from experimental NOE spectra with the use of the full relaxation matrix approach.
"O" - Protein crystallographic package
PROTEIN - Program system for the crystal structure analysis of macromolecules.
TALOS - A database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence.
X-PLOR

2.) Imaging Softwares

OpenDX - (IBM) Visualization Data Explorer
C3D - 3D imaging
NIH-IMAGE - public domain image processing and analysis program for Mac
NIH-IMAGE for windows

3.) Molecular Dynamics softwares

AMBER - Assisted Model Building with Energy Refinement
CHARMM
Discover - Molecular Simulations
GROMOS
MacroModel - Graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution.
NAMD

4.)Molecular Graphics & Visualization Softwares

BRAGI - Interactive protein-modelling program
Cn3D - Allows to view 3-dimensional structures from NCBI's Entrez database
GRASP - Graphical Representation and Analysis of Structural Properties
InsightII - Molecular Simulations
MidasPlus - Molecular Display and Simulation System
MOLDEN - Package for displaying Molecular Density
MSV - Molecular Surface Viewer
MOLMOL
MOLPRO
MOLPRO
MolScript
ORTEP - Crystal Structure Illustrations
PovChem - Molecular graphics software
PREPI - Protein REPresentations Interactively
RasMol
Raster3D - Biomolecular Structure
RIBBONS
SPARTAN - Molecular modelling and visualisation program suite
SPOCK - Molecular graphics program
SYBYL
WebLab Viewer Pro/Lite - Molecular Simulation
WHATIF - 3D modelling services
VMD

5.) NMR processing and analysis softwares

AURELIA - Software for semi-automated analysis of all types of 2D, 3D and 4D spectra.
CORMA (COmplete Relaxation Matrix Analysis) - FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment.
CROSREL - Program for the analysis of ROESY and NOESY NMR data.
DASHA - Model-Free Analysis of Protein Dynamics from Heteronuclear NMR Relaxation Data
DSYMPC - NMR SIMULATION AND ITERATION TOOLS FOR PCs
FELIX - NMR data processing, analysis and assignment program (Molecular Simulations).
FIRM - Interactive program for calculating NOEs of a structural model using the relaxation matrix approach. Distances, corrected for the effects of spin diffusion, can be back-calculated from experimetal NOEs using a hybrid relaxation matrix. Includes features for simulating internal motions.
GAMMA - A library written for simulation of Nuclear Magnetic Resonance experiments"
Gifa - A multi-purpose NMR program, designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets.
MARDIGRAS - Matrix Analysis of Relaxation for DIscerning the Geometry of an Aqueous Structure, program for calculating proton-proton distances from cross-peak intensities measured from a 2D NOE experiment.
MestRe-C - A program designed to process and plot 1D NMR spectra on PC’s running Windows 95/98/NT 4.0. It imports files from most spectrometers and includes a number of useful tools .
MEX and CIFIT - For simulation of exchanged-broadened lineshapes for uncoupled spin systems (MEX) and to analyse selective inversion experiments (Hoffman-Forsen) for slow chemical exchange (CIFIT).
Modelfree - Program to fit the extended model free spectral density function to NMR spin relaxation data.
MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation. MORASS uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzes 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained.
NMRPipe - NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis.
NUMARIT - A spin simulation/iteration package for the X32.
PERCH - (PEak reseaRCH) - an integrated NMR-software package for research, analytics and education. The spectral analysis and simulation up to 10 spins is based on the program MLDC (Modified LAOCOON with Dipolar Couplings).
PC Software: APT, DECAY, DEPT, FIDUNK, FTNMR Simulator, HETJ-2D, HOMOJ-2D, IRREADER, NMRSM, UNKINP, XHCORR .
PRONTO - The PROtein Nmr TOol .
RMN - A Nuclear Magnetic Resonance (NMR) data processing program for the Mac.
SIMPSON - (SIMulation Package for SOlid-state Nmr spectroscopy) - A solid-state NMR simulation program with emphasis on ease of use. Multiple pulses, spins, and dimensions. Input files written in Tcl demonstrate simulations of 20 major solid-state experiments.
Sparky - Graphical NMR assignment program for proteins and nucleic acids. Runs under Windows, Linux, or Unix.
SwaN-MR - An NMR processing software for the Macintosh. It reads 1D, 2D, 3D and 4D spectra coming from many spectrometers and its feature list is comparable to those of commercial packages.
V - an interactive software system for MR signal processing. Source
VNMR - Software package for Varian NMR spectrometers.
XEASY - ETH Automated Spectroscopy based on the X Window System to satisfy the requirement for NMR spectrum analysis.
XWIN-NMR - software package sits of BRUKER spectrometers.

6.) Protein & DNA - Structure & Sequence analysis Softwares

CURVES - Helical analysis of irregular nucleic acids
DELILA - Software for Information Analysis of Protein and Nucleic-acid Sequences
DSSP - Protein secondary structure assignment program
Dotter - A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis
Modeller - Program for homology protein structure modelling by satisfaction of spatial restraints
PROCHECK
PROCHECK_NMR
SQUID

7.) Protein properties computation softwares

DelPhi - Finite Difference Poisson-Boltzman Solver
MGMS - Molecular Surfaces Computation

8.) Quantum mechanical computation softwares

AMSOL - Semiempirical quantum chemistry program
Jaguar - ab initio software package
GAMESS
GAUSSIAN
MOPAC - Semiempirical quantum chemistry program
MOPAC 2000
QCPE - Quantum Chemistry Program Exchange
TURBOMOLE - Program Package for ab initio Electronic Structure Calculations

9.) Receptor-ligand interactions Softwares

DOCK - Docking of flexible ligands into protein target
FlexX - Automatic prediction of receptor-ligand interactions
FlexS - Automatic structural alignment of small organic molecules
TINKER - Software Tools for Molecular Design

10.) Scientific softwares

gnuplot - An Interactive Plotting Program
NLREG - Nonlinear Regression Analysis Program

BioImageXD - FREE BIOMEDICAL SOFTWARE

BioImageXD - free open source software for analysis and visualization of multidimensional biomedical images

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images.

BioImageXD is a collaborative open source free software project, designed and developed by microscopists, cell biologists and programmers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG, Dresden, Germany and collaborators worldwide.

BioImageXD is written in Python and C++, using wxPython for the GUI, and leverages the power of the Visualisation Toolkit (VTK) for multi dimensional image processing and 3D volume rendering. BioImageXD also uses the Insight Toolkit, ITK for segmentation and other image porocessing tasks. BioimageXD works on Linux (or theoretically any UNIX with wxPython and VTK), Mac OS X 10.5, and MS Windows XP/2000 (possible Vista).

FEATURES

BioimageXD currently offers you, as a microscopy or other scientist, working with single or multi channel 2D, 3D or 4D (time series) image data

1.)IMAGE VIEWING

Open data in common microscopy formats (or images or stacks of images, and time series), and view the data image by image. Supported data formats include:

Carl Zeiss .lsm files
OlympusFV1000 .oif
Leica confocal microscope data files SP2 .txt and SP5 .lif
numbered image stacks import
VTK XML Image files

Image viewing is roughly comparable to the free Carl Zeiss, Olympus, Leica and other commercial image viewers, but with very realistic 3D rendering without artifacts from the graphics card - using ray cast 3D mode. Viewing modes avaialble are: Slices, orthographic sections, maximum intensity projection and 3D rendering. Time series data are supported.

2.) IMAGE PROCESSING

Adjust colour / brightness / contrast / gamma, change colour or palette of a dataset/channel, filter out noise, correct for fluorescence bleaching in time series data.

3D segmentation and object ananlysis.

3.) 3D VOLUME RENDERING

3D datasets can be interactively volume rendered, using :

i.)software ray casting (slower but prettiest. Accelerated by having many processors)
ii.)OpenGL graphics card texture mapping (faster but lower resolution - depending on texture menory size)
iii.)TeraRecon Inc. VolumePro1000 hardware ray casting board.

The colour and opacity transfer functions are fully user defined. You can volume render a merged multi channel RGB dataset to see colocalisation in 3D, or render a 3D colocalisation map. BioImageXD uses the VTK interface with OpenGL. We plan to enable Hardware Stereo viewing (quad buffered page flipping and red-blue anaglyph, and other modes). You will be able to break out those 3D glasses and really "see" your data! This is the future of 3D microscopy.

4.) MOVIE MAKING

Use the Animator module to set up a camera path around your 3D data, and make a movie of it spinning and fly though zooming any way you like. Time series data are supported: "4D data".

5.)Colocalisation analysis

Colocalisation tool allows you to analyse the colocalisation of signal intensity in a multi channel 3D data set, avoiding the problem of false colocalisation seen in z-stack projection images, and perform some statistical analyses that give you hard numbers about the amount and quality of colocalisation in your data. Uses similar algorithms to those in imageJ, for instance the WCIF plugin for Automatic Colocalisation Thresholds, using the method of Costes et al.

Manders coefficients and statistical significance analysis, with 2D histogram/scatterplot and results statistics export.

Click here to download this free software.

Download 30-Day Trial Version of NI LabVIEW 2009

LabVIEW is a graphical programming environment used by millions of engineers and scientists to develop sophisticated measurement, test, and control systems using intuitive graphical icons and wires that resemble a flowchart. LabVIEW offers unrivaled integration with thousands of hardware devices and provides hundreds of built-in libraries for advanced analysis and data visualization. The LabVIEW platform is scalable across multiple targets and operating systems, and since its introduction in 1986 has become an industry leader.

Click here to download 30 day trial version of LabVIEW 2009 software.