A 3D surface and volumetric mesh generator for MATLAB/Octave
A simple yet powerful mesh generator based on MATLAB/GNU Octave language, creating finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows.
A Numerical MRI Simulation Platform
The MRiLab project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MRiLab/ The MRiLab is a numerical MRI simulation package. It has been developed and optimized to simulate MR signal formation, k-space acquisition and MR image reconstruction. MRiLab provides several dedicated toolboxes to analyze RF pulse, design MR sequence, configure multiple transmitting and receiving coils, investigate magnetic field related properties and evaluate real-time imaging technique. The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961
Virtual X-Ray Imaging Library on GPU
gVirtualXRay is a C++ library to simulate X-ray imaging. It is based on the Beer-Lambert law to compute the absorption of light (i.e. photons) by 3D objects (here polygon meshes). It is implemented on the graphics processing unit (GPU) using the OpenGL Shading Language (GLSL). SimpleGVXR is a smaller library build on the top of gVirtualXRay. It provides wrappers to Python2, Python3, R, Ruby, Tcl, C#, Java, and GNU Octave.
Volumetric image processing software
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET).
Scientific Visualisation Made Easy
The Simple Medical Imaging Library Interface (SMILI), pronounced 'smilie', is an open-source, light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images, vector images, DICOMs, anonymizing, shape analysis and models/surfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing, thresholding, masking etc. images and models, both with graphical user interfaces and/or via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level (Qt) interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit (ITK) and Visualisation Toolkit (VTK). The framework allows one to build stand-alone medical imaging applications quickly and easily.
This project, developed at UCL London, provides code for tomographic reconstruction. NiftyRec is written in C and has Python and Matlab extensions. Computationally intensive functions have a GPU accelerated version based on CUDA.
This project is the implementation of The Virtual Collaborative Environment (VCE) which supports clinical applications of 3D modeling in medicine. The system is based on three layer client-server architecture.
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations.
Gestion de Cabinet Medical / Medical Patient Record
Since 2 months, new version will arrive in QT5, with better integration of multimedia document and multilanguage support. If you have some specificity in your country, tell us we can integrate it. Medintux est une suite logicielle pour la gestion du cabinet médical et des services hospitaliers. Agrément ROSP, Compatible HAS avec le Vidal ou Thériaque, CIM10, codage CCAM. Liaison Sesam Vitale, Hprim, Apicrypt, Sigems. 100% Paramétrable et personnalisable. Environnement : Fonctionne sous MAC, Linux, PC, Android et mode Web intégré dans un navigateur. Fonctionnalités : Comptabilité, Gestion du dossier patient, Gestion documentaire, Gestion des admissions et des salles d'attentes. Aide à la prescription.... Base de donnée : Gestion client serveur avec Mysql. Supporte des milliers de dossiers sans ralentissement. Une communauté active avec plusieurs centaines d'utilisateurs au quotidien. Medintux est un projet mature utilisable au quotidien
NBT is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki with extensive help and tutorials.
Toolbox for processing spinal cord MRI data
The Spinal Cord Toolbox is a comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. List of contributors can be found here: https://sourceforge.net/p/spinalcordtoolbox/wiki/Home/
Library to support quantitative analysis of radiotherapy data
Moved to: http://github.com/MIC-DKFZ/RTTB RTToolbox is a software library, developed at the DKFZ to support quantitative analysis of treatment outcome for radiotherapy. The RTToolbox was designed following object-oriented design principles and was implemented in the language C++. It supports the import of radiotherapy data (e.g. dose distributions and structure sets) from DICOM-RT format and other standard image processing formats by using a bridge to ITK. The RTToolbox supports the full range of radiotherapy evaluation. Tools such as DVH calculation, arithmetic operations on dose distributions and structure relationship analysis are provided as a basis for further calculations. Dose comparison indices such as Conformity Index (CI), Homogeneity Index (HI) and Conformation Number (CN), and biological models including TCP, NTCP, EUD and BED are determined from dose distributions and DVHs. The RTToolbox can be easily extended to support other data format, comparison indices and
The openLBMflow is an fast fluid flow solver based on Lattice Boltzmann Method. Main future are 2D and 3D code, single and multiphase models, Output data in VTK format can be directly open in Paraview. Download Windows or Linux binary version now.
KinetDS is a software for curve fitting particularly designed for kinetic (mechanistic and empirical) description of a substance dissolution from solid state. It was primarily designed for handling pharmaceutical dissolution tests
A Multi-functional GUI-based Program for Image Processing and Analysis
The MatrixUser project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MatrixUser/ Most of the medical images (e.g. CT, MRI, PET, etc.) comprises multiple frames which represent slices, phases, timing etc. from the same imaging object. Those images can be saved as multidimensional matrices in Matlab thanks to Matlab's powerful support of multidimensional data representation. However, within Matlab, most of image manipulation functions are limited or tailored for processing two-dimensional matrix. The MatrixUser is a software package which features functions designed and optimized specifically for manipulating multidimensional real or complex data matrix. MatrixUser provides a nice graphical environment for easily performing image analysis tasks including multidimensional image display, matrix (image stack) processing and rendering etc. MatrixUser is a great lightweight tool for users who are working in image processing field under Matlab.
Medical Image Reconstruction Framework
Medical Image Reconstruction Framework
Safe, open source brain stimulation for everyone!
OpenStim is a set of open-source hardware and software designed to administer transcranial direct current stimulation for less than $50. IMPORTANT NOTICE Recently, an error was discovered in the documentation page describing the commands for setting the stimulation polairty. The documentation originally indicated that setting operating_power to a positive number would set the output from W6 as the anode. This is not correct for the most recent version of OpenStim and has been corrected. Note that the correct cofngiuration is: If operating power is set to a positive number the output from the digital potentiometer (W6) should be the cathode If operating_power is set to a negative number, W6 should be the anode
To envision the radiation exposure in Neutron Activation Experiments
A software called Activity Predictor is developed using Java TM programming language. The Activity Predictor calculates activities, exposure rates and gamma spectra of activated samples for NAA experiments. The calculation procedure for predictions involve both analytical and Monte Carlo methods. The Activity Predictor software is validated by a series of activation experiments. It has been found that this software calculates the activities and exposure rates precisely. The software also predicts gamma spectrum for each measurement. The predicted spectra agreed partially with measured spectra. This software has a XML database which includes nuclear data for frequently used materials in NAA. Neutron Neutron cross section data from ‘‘ Tables for Neutron Activation Analysis’’ , photon cross section data from Berger and Hubbell’s XCOM photon cross sections database [ 2], and isotope decay from from Lund/LBNL database are included in this database.
MRI Multiple Echo T2 Analysis
Users load multiecho MRI data and draw ROIs. AnalyzeNNLS creates a T2 distribution from the averaged decay data. Regional fractions and geometric T2 times can be determined. Please reference: Bjarnason TA, Mitchell JR. JMR 206:200-4 (2010). Temporal Phase Correction included in version 2.5. If you use this functionality, please reference: Bjarnason TA, Laule C, Bluman J, Kozlowski P. JMR 232:22-31 (2013).
Modular Image Processing in Python
MIPPY is a minimalistic DICOM image browser with built-in image processing modules. Its modular design means it can be extended with any number of user-created modules for image processing and analysis.
KAP evaluation and patient records in radiodiagnostic
This program tries to help radiologists to keep track of patients which receive radiation doses (measured, or computed, free in air) from radiodiagnostic examinations. It performs computation of KAP (kerma-area-product if it is not recorded by a dedicated DAP-meter) and record the patient information. The program also generates elegant reports which can be converted as pdf, xls etc. Source code included in jar files. Also, available on GitHub: https://github.com/ZiliasTheSaint/PatientRxRecord.git
CT collimation measurements using CR plates. Please reference Bjarnason TA, Yang CY. CT radiation profile width measurement using CR raw data. Journal of Applied Clinical Medical Physics. 2015;16:501-507. Available from: http://www.jacmp.org/index.php/jacmp/article/view/5512
ISMRM Raw Data File Format
We have moved to GitHub. web: http://gadgetron.github.io code: http://github.com/gadgetron/gadgetron discussion board: https://groups.google.com/forum/#!forum/ismrmrd
Scientific Image and Signal Analysis in Java
IQM has moved to GitHub https://github.com/iqmmug/iqm
Lightweight, RESTful DICOM server for healthcare and medical research
[2015-06-12] Orthanc has left SourceForge. All the downloads are now available directly from our official Website: http://www.orthanc-server.com/browse.php