[heading style=”2″] SOFTWARES [/heading]

Software: HHsim: Graphical Hodgkin-Huxley Simulator

HH Simulator Screenshot


HHsim is a graphical simulation of a section of excitable neuronal membrane using the Hodgkin-Huxley equations. It provides full access to the Hodgkin-Huxley parameters, membrane parameters, stimulus parameters, and ion concentrations.

To download the appropriate version of HHsim for your Windows/Mac, click here.

To view tutorials for this software, click here.





Software: ITK-SNAP


ITK-SNAP Screenshot

SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Some of the core advantages of SNAP include

  • Linked cursor for seamless 3D navigation
  • Manual segmentation in three orthogonal planes at once
  • Friendly UI for selecting active contour segmentation parameters
  • Support for many different 3D image formats, including NIfTI
  • Support for concurrent, linked viewing and segmentation of multiple images
  • Limited support for color images (e.g., diffusion tensor maps)
  • 3D cut-plane tool for fast post-processing of segmentation results
  • Extensive tutorial

If you are a clinical researcher in neurology, radiology, psychiatry, surgery, or any other field that uses medical images, you may be able to use ITK-SNAP to enhance your productivity. Unlike many current image processing tools, ITK-SNAP was designed to be easy to learn and use for people without a computer science or engineering background.

If you are in the business of developing software applications that work with medical images, you may be able to incorporate parts of SNAP into your software. You can also use SNAP as a model of a user friendly application developed on top of ITK.

ITK-SNAP is free software, provided under the General Public License.

To download the appropriate version of ITK-SNAP for your Windows/Mac, click here.

To view tutorials for this software, click here.



Software: GIMIAS (Graphical Interface for Medical Image Analysis and Simulation)


GIMIAS (Graphical Interface for Medical Image Analysis and Simulation) is a software framework designed to be an integrative tool for fast prototyping of medical applications. It is a workflow-orientedenvironment for advanced biomedical image computing and simulations, and it can be extended through the development of problem-specific plug-ins.

Visualization of fibers orientation in left ventricle

GIMIAS is particularly tailored to integrate tools from medical imaging, computational modeling, numerical methods and computer graphics to provide scientific developers and researchers with a software framework for building a wide variety of tools. Multi-modal image processing, personalized model creation, numerical simulation and visualization of simulation results are some of the possible applications for which GIMIAS has been designed. The aim of this framework is to combine tools from different areas of knowledge providing aframework for multi-disciplinary research and clinical study.

GIMIAS allows building medical prototypes for clinical evaluation, in the areas of medical image analysis, modeling and simulation. It simplifies the integration of tools needed to build new clinical workflows, and the use of common libraries for user interfaces, visualization, image processing, DICOM access etc, that are commonly used as standard in Virtual Physiological Human (VPH) research.

Visualization of flow within a vessel

The prototypes developed on GIMIAS can be verified by end users in real scenarios and with real data at early development stages, thus reducing the time and effort required to get new concepts from research to the clinical environment.

GIMIAS provides a graphical user interface with all main data IO, visualization and interaction functions for images, meshes and signals. It includes additional tools for image segmentation, mesh editing, signal navigation and specific visualizations.

GIMIAS provides a simple Application Programming Interface (API) that allows developers to create their own tools as plug-ins that can be dynamically loaded and combined in different ways to create specific applications. GIMIAS API provides developers with standard services such as rendering, data access and advanced visualization of multi-modal imaging data, among others.

To download the appropriate version of GIMIAS for your Windows, click here.

To view tutorials for this software, click here.



Software: BioSig


BioSig is an open source software 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. Major application areas are: Neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems and sleep research. The aim of the BioSig project is to foster research in biomedical signal processing by providing open source software tools for many different applications. Generally, many concerns have to be addressed in this scientific field. BioSig handles this by providing solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, data visualization, and so on.

BioSig consists of some (more or less) coherent parts, for more details take a look at the project page:

  • BioSig for Octave and Matlab (biosig4octmat): A toolbox for Octave and Matlab with powerful data import and export filters, feature extraction algorithms, classification methods, and a powerful viewing and scoring software.
  • BioSig for C/C++ (biosig4c++): A C/C++ library that provides reading and writing routines for different biosignal data formats.
  • rtsBCI (rtsbci): A real-time BCI system implemented in Matlab and Simulink.
  • BioProFeed (bioprofeed)
  • BCIx (bcix)
 To download the appropriate version of BioSig for your Windows/Linux, click here.



Software: ODIN – Object Oriented Development Interface for NMR


ODIN is a C++ software framework to develop and simulate magnetic resonance sequences. Contemporary magnetic resonance imaging techniques are available, for example sequence modules for echo-planar imaging and spiral-imaging, parallel imaging with GRAPPA reconstruction, two-dimensional pulses and field-map-based distortion corrections. All common steps, from compiling your sequence to plotting or simulating it, can be performed within a graphical user interface. Written in C++ with an object-oriented design, ODIN is very modular, flexible and requires very little code to write: The sequences that come with ODIN are easy to understand and modify.



Some highlights of ODIN:

– Plotting of the sequence timecourse in a graphical user interface.

– Simulating the spin-physics of the sequence (Bloch-Torrey equations) using a virtual phantom to generate a virtual MR signal. System imperfections (eddy currents, B1 inhomogeneity, noise) can be switched on/off at will during the simulation.

– Visualization of the k-space trajectory, b-values, eddy currents, etc.

– Highly-customizable, multi-threaded image reconstruction framework.

To download the appropriate version of ODIN for your Windows, click here.

To view tutorials for this software, click here.

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