MATLAB TECHNICAL KIT

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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.

Free medical imaging softwares, applications and resources

If you work with medical imaging files, the site "I DO IMAGING" can help you. Looking for a free DICOM viewer, DICOM converter, or PACS client? You'll find them there.It tracks free medical imaging applications and resources: conversion programs, image display and analysis, surface and volume rendering, PACS clients and servers. Many programs are classified by a speciality to allow you to find similar programs by imaging modality, medical specialization, or similar. Half of all the programs listed there work with DICOM files, but there are over 25 file formats covered.

All the programs included are free and intended for distribution; there are no "demo" versions of commercial applications. If you are involved in programming, many of the programs are open-source, and provide APIs and SDKs for radiology programmers.

4 Day course on IDL & Medical Imaging

Benefits:
Learn how to use IDL's image analysis and visualization power.
Use the DICOM capabilities of the IDL DICOM Toolkit and the DICOM Network Services add-on modules efficiently.

Topics:
Medical Image Processing, Image Segmentation,
Image Fusion
Create Graphical User Interfaces for your applications
Profit from IDL iTools
Read and write Dicom files
Communicate within a DICOM Network

Pre-requisites: Programming experience in IDL.

Duration: 4 Days

Location:
CREASO Training Center in Gilching, Germany,
or customer’s site (worldwide).

Contact Details :
Klaus Löschinger +49-8105-378-123
Doris Lutzeier +49-8105-378-122
E-Mail: k.loeschinger@creaso.com

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 ADVANCED MEDICAL VISUALIZATION SOFTWARES

1.) 3Di

3Di is a novel cloud computing platform for advanced (3D) visualization and analysis of medical images. With zero upfront cost, 3Di turns any internet PC to a full feature advanced visualization workstation - delivering both image data, visualization and analysis tools.



2.) 3Dnet Suite

3DNet Suite is a proven multi-purpose medical imaging application suite, which offers an extensive set of tools for clinical data analysis. It accepts DICOM compliant images from most aquisition devices. The complete imaging product family has multilingual support. The Suite is a totally interactive tool, designed for 2D and 3D reconstruction of small and large data.



3.) DynaCAD for Prostate

DynaCAD for Prostate is a digital imaging system with a comprehensive set of advanced visualization tools for performing real-time image analysis of prostate MRI studies.



4.) DynaSuite Neuro

DynaSuite Neuro - Automated Processing for Optimized Workflow DynaSuite Neuro is a high performance advanced MR neuro solution by Invivo, designed for optimal workflow and repeatable analysis for pediatrics and adults. The data is automatically processed and displayed in predefined layouts which are customizable for the physicians preference. The simplified user interface provides the neuroradiologist with the tools to analyze perfusion (PWI), diffusion (DWI) and functional MRI (fMRI) quickly and easily.



5.) FiatLux Visualize

FiatLux Visualize delivers the ability to interactively manipulate CT and MR patient data in real-time. Most PCs, laptops and tablets readily support the rich graphics delivered by FiatLux Visualize, allowing the ability to view images in the office, at home, or at the patient bedside.



6.) Multilayer3D PRO

Multilayer3D PRO is an advanced 3D GIS (Radar) visualization system for environmental and structural monitoring.



7.) PercuNav Software

The Traxtal PercuNav system represents a new class in Image Guided Intervention (IGI) equipment. It is the first FDA cleared IGI system to track the tips of needles. It seamlessly integrates preoperative with live images, showing the tool location superimposed on the images.



8.) Vision Tools 3Dview

Vision Tools 3Dview is a powerful and scalable MPR/MIP/3D reconstruction software for CT and MRI modalities that can present high quality 3D volumes with multiple color editing utilities.



9.) Vitrea Software

Vitrea Enterprise Suite is Vital Images’ premier package of advanced visualization tools, clinical applications and data management systems. These scalable solutions integrate seamlessly with PACS, and are available across your enterprise, via the Web, and on both thin- and thick-client technologies.



10.)Ziostation

Ziostation includes all the tools necessary to analyze case types from the basic to the advanced. The clinical applications are 3D, 4D, MIP, MPR, CPR, Multi-Modality Viewer, Multi-volume fusion, Vessel analysis, Coronary analysis, Colon analysis,PET/CT viewer, CT Cardiac Function Analysis, CT Brain Perfusion, Calcium Scoring, Reporting functions.

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