Medical simulation

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Medical simulation and visualization frameworks

  • SOFA: The Simulation Open Framework Architecture (SOFA) is an efficient simulation framework dedicated to research in medical simulation and also used to develop new training technologies.
    • SOFA is open source (mostly under LGPL) and hosted on GitHub.
    • SOFA gathers about 10 years of research in physics simulation. Many publications have been accepted, several simulators have been developed and five startups have been created. The research topics have been diverse, including (1) Solid mechanics with the simulation of the brain, the ear, the bones, the heart, the liver, (2) Fluid dynamics with the simulation of fat filling and blood flow in aneurysms, Thermodynamics with thermo-ablation of tumors, and (3) many other topics as image processing, animation or biological applications
    • https://www.sofa-framework.org/
  • SimVascular: The only fully opensource software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.
  • 3DSlicer: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. 3D Slicer is:
    • A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.
    • A free, open source software available on multiple operating systems: Linux, MacOSX and Windows
    • Extensible, with powerful plug-in capabilities for adding algorithms and applications. Features include:
      • Multi organ: from head to toe.
      • Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy.
      • Bidirectional interface for devices.
    • https://www.slicer.org/wiki/Main_Page
  • MITK: The Medical Imaging Interaction Toolkit (MITK) is a free open-source software system for development of interactive medical image processing software. MITK combines the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) with an application framework. As a toolkit, MITK offers those features that are relevant for the development of interactive medical imaging software covered neither by ITK nor VTK, see the Toolkit Features for details.
  • NIFTK - A TRANSLATIONAL IMAGING PLATFORM
    • NifTK is the name of the platform developed at the Univeristy College London (UCL), combining NiftyReg, NiftySim, NiftyRec and NiftySeg via the viewer NiftyView. The aim is to take the tools that TIG/CMIC develops, and apply them in a clinical context.
    • http://cmictig.cs.ucl.ac.uk/research/software/software-nifty
  • GIMIAS: the Graphical Interface for Medical Image Analysis and Simulation (GIMIAS)is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.
    • GIMIAS is built over widely used open source C++ based libraries like the Visualization Toolkit (VTK, suported by Kitware Inc.), the Insight Toolkit (ITK, also supported by Kitware Inc.), the DICOM Toolkit (DCMTK, supported by Offis in Germany), the Medical Imaging Interaction Toolkit (MITK, developed at Division of Medical Informatics, Deutsches Krebsforschungszentrum (DKFZ), Germany) and other commonly used C++ libraries (Boost, wxWidgets, CXXTest, among others).
    • GIMIAS is released under a BSD License to allow cooperation between different institutes and developers.
    • http://www.gimias.org/


X rays

  • XRAYSIM: http://xraysim.sourceforge.net/index.htm
    • XRaySim is a free, open-source simulation package for use in Industrial Non-Destructive testing and medical imaging applications. It is currently available for Microsoft Windows, and (technically) for Linux. Pre-compiled binaries are distributed for Windows only, though the code is platform-independent and should compile on most Linux distributions. Learn more about XRaySim or check out the documentation to understand what it can do and gauge its capabilities.
    • XRaySim is being actively developed and maintained by Koushik Viswanathan It includes several custom modules,including a GPU accelerated simulation and complete image reconstruction framework.
  • gVirtualXRay: http://gvirtualxray.sourceforge.net/gvirtualxray.php
    • Virtual X-Ray Imaging Library on GPU
    • This project is focused on developing new software technologies for simulating X-ray images on the graphics processor unit (GPU) using OpenGL. It supports ‘old’ OpenGL implementation as well as modern OpenGL core profile (OpenGL 3.2+). No deprecated function in OpenGL has been used. The library takes care of matrix transformations, matrix stacks, etc.
    • See https://hal.inria.fr/hal-01266065/document

Computed tomography

  • CTSIM: http://www.ctsim.org/
    • CTSim simulates the process of transmitting X-rays through phantom objects. These X-ray data are called projections. CTSim reconstructs the original phantom image from the projections using a variety of algorithms. Additionally, CTSim has a wide array of image analysis and image processing functions.
    • CTSim is Copyright © 1983-2014 by Kevin M. Rosenberg, M.D. and is open-source software under the GNU Public License.

Ultrasound

  • FIELD II: http://field-ii.dk/
    • Field II is a program for simulating ultrasound tranducer fields and ultrasound imaging using linear acoustics. The programs uses the Tupholme-Stepanishen method for calculating pulsed ultrasound fields. The program is capable of calculating the emitted and pulse-echo fields for both the pulsed and continuous wave case for a large number of different transducers. Also any kind of linear imaging can be simulated as well as realistic images of human tissue. The program is running under Matlab on a number of different operating system (Windows, Linux, Mac OS X), and the programs are currently free to use under certain restrictions (see copyright).
    • The latest release of the program is version 3.24 of May 12, 2014. Note that this code will work with Matlab 8.20 under Linux, Mac and Windows in 64 bits versions.
    • The development of the professional version Field IIpro has now been completed and all commands and modes are now parallelized. It takes advantage of the multi-core capabilities of modern CPUs. The central part of the program’s calculation routines and its memory management has been re-written for optimizing speed on multi-core CPUs. This has both increased single-core and multi core execution. For a 12 cores machine a speed up of a factor of nearly 25 can be attained. A general speed-up is attained by a factor between 1.5 and 3 for single core processing compared to the free Web version. Multiple cores can be used and the calculation speed scales roughly proportional to the number of physical cores
    • Included in the Virtual Imaging Platform: https://www.egi.eu/use-cases/scientific-applications-tools/virtual-imaging-platform/
  • ABERSIM: https://www.ntnu.edu/isb/ultrasound/abersim
    • Abersim© is a toolkit for simulating 3D nonlinear acoustic forward wave propagation through an attenuating medium. It is designed for use within the field of medical ultrasound imaging, but this does not exclude other areas. It has a MATLAB interface, which enables the use of MATLAB for visualization, pre- and post processing. The core routines have been implemented in C for efficiency, and to take advantage of MPI parallel computing resources.
    • Abersim© offers:
      • A simulation program for 3D nonlinear medical ultrasound acoustic wave propagation for arbitrary pulses and arbitrary transducer geometries. Includes frequency dependent absorption and models of heterogeneous tissue.
      • A large degree of freedom for the user to specify input pulses and pulsing schemes.
      • All source code available.
      • Comes in a pure MATLAB version, a MATLAB + core routines in C compiled via the MATLAB MEX interface, and a stand-alone C version for batch processing.
      • Parallellized C version using MPI (Message Passing Interface) for use on clusters or supercomputers (to be released soon).
    • The Abersim software is currently not maintained or updated. The C-version is currently outdated and relies on old libraries making the compilation process difficult. An overhaul is planned in near future.
  • K-WAVE: http://www.k-wave.org/index.php
    • k-Wave is an open source acoustics toolbox for MATLAB and C++ developed by Bradley Treeby and Ben Cox (University College London) and Jiri Jaros (Brno University of Technology).
    • The software is designed for time domain acoustic and ultrasound simulations in complex and tissue-realistic media. The simulation functions are based on the k-space pseudospectral method and are both fast and easy to use. The toolbox includes:
  1. An advanced time-domain model of acoustic wave propagation that can account for nonlinearity, acoustic heterogeneities, and power law absorption (1D, 2D, and 3D)
  2. The ability to model pressure and velocity sources, including photoacoustic sources, and diagnostic and therapeutic ultrasound transducers
  3. The ability to specify arbitrary detection surfaces with directional elements, with options to record acoustic pressure, particle velocity, and acoustic intensity
  4. An optimised C++ version of the code that maximises computational performance for large simulations
  5. The option to use the forward model as a flexible time reversal image reconstruction algorithm for photoacoustic tomography with an arbitrary measurement surface
  6. A fast, one-step, photoacoustic image reconstruction algorithm for data recorded on a linear (2D) or planar (3D) measurement surface
  7. Optional input parameters to adjust visualisation and performance, including options to generate movies and to run the simulations on a graphics processing unit (GPU)
  8. An extensive user manual and many simple to follow tutorial examples to illustrate the capabilities of the toolbox
  • FOCUS: http://www.egr.msu.edu/~fultras-web/
    • FOCUS is a free cross-platform ultrasound simulation tool that quickly and accurately calculates pressure fields generated by single transducers and phased arrays.
    • FOCUS now has B-Mode imaging simulations, includes cyst phantom examples with linear and curved arrays
    • FOCUS is simple to use for both experts and non-experts from any supported version of MATLAB.

Commercial medical ultrasound simulators

General info

Magnetic Resonance Imaging (MRI)

  • ODIN: http://od1n.sourceforge.net/index.html
    • ODIN is a C++ software framework to develop and simulate magnetic resonance sequences.
    • It is State-of-the-Art: 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.
    • Easy-to-Use: All common steps, from compiling your sequence to plotting or simulating it, can be performed within a graphical user interface.
    • Truly Object-Oriented: 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.
    • Open Source: ODIN is a free software framework. It contains well-established techniques in magnetic resonance which were documented in scientific publications. It can be used and modified without restrictions.
    • Included in the Virtual Imaging Platform: https://www.egi.eu/use-cases/scientific-applications-tools/virtual-imaging-platform/
  • MRISIMUL: http://mri.dib.uth.gr/
    • MRISIMUL is a step-by-step comprehensive Bloch equation simulator which integrates realistic aspects of the MRI experiment from signal generation to image formation. This simulation platform allows its application in large-scale analysis by employing GPU technology. The high performance of MRISIMUL allows its application without model simplifications and with no assumptions with respect to the underlying pulse sequence.
    • MRISIMUL allows the development of custom MRI pulse sequences and their application on 3D computer models of realistic objects. MRISIMUL was developed in MATLAB (The Mathworks Inc., Natick, MA) while the computationally demanding core services (kernel) were developed in CUDA-C (NVIDIA, Santa Clara, CA) and executed in parallel within the graphic processing unit (GPU) environment.
  • JEMRIS: http://www.jemris.org/
    • JEMRIS is an extensible MRI simulation framework which provides an MRI sequence development and simulation environment for the MRI community. The development was driven by the desire to achieve generality of simulated 3D MRI experiments reflecting modern MRI systems hardware. The accompanying computational burden is overcome by means of parallel computing. Many aspects are covered which have not hitherto been simultaneously investigated in general MRI simulations such as parallel transmit and receive, important off-resonance effects, non-linear gradients, and arbitrary spatiotemporal parameter variations at different levels. The latter can be used to simulate various types of motion, for instance. The JEMRIS user interface is very simple to use but, nevertheless, it presents few limitations. MRI sequences with arbitrary waveforms and complex inter-dependent modules are modelled in a GUI-based environment requiring no further programming.
  • SpinBench: http://www.heartvista.com/spinbench/
    • Downloadable but apparently not open-source. Plugin APIs are available
    • SpinBench™ is a software environment designed for the rapid prototyping and analysis of magnetic resonance imaging experiments. MRI pulse sequences can be easily defined and simulated in a variety of ways, all through a graphical user interface. SpinBench is also useful as a teaching tool for courses covering MRI spin physics.
    • While most sequences can be implemented without significant coding, additional modules can be added to provide unique capabilities. Sequences can be graphically simulated quickly, reducing development time.
  • SIMRI: https://sourceforge.net/projects/simri/
    • SIMRI: a versatile and interactive Magnetic Resonance Imaging (MRI) simulator.Such a simulator is a command line software written in C that reproduces the physical phenomenas encountered during an MRI acquisition to produce a realistic MRI image.
    • Development apparently frozen

Other information

GATE (CT, SPECT, PET, Optical, Radiotherapy)

GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging (Bioluminescence and Fluorescence) and Radiotherapy experiments. Using an easy-to-learn macro mechanism to configurate simple or highly sophisticated experimental settings, GATE now plays a key role in the design of new medical imaging devices, in the optimization of acquisition protocols and in the development and assessment of image reconstruction algorithms and correction techniques. It can also be used for dose calculation in radiotherapy experiments.

http://www.opengatecollaboration.org/home

Included in the Virtual Imaging Platform: https://www.egi.eu/use-cases/scientific-applications-tools/virtual-imaging-platform/

Other PET simulators

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