Matlab toolboxes for medical image analysis
CCP SyneRBI is a collaborative computational project in synergistic reconstruction for biomedical imaging. Its main software package SIRF is an open-source framework for synergistic image reconstruction.
un0rick: open source pulse echo ultrasound
This project has a specific target of providing a low-cost, open source technological kit to allow scientists, academics, hackers, makers or OSHW fans to hack their way to ultrasound imaging – below 500$ – at home, with no specific equipment required.
Halbach array magnet for in vivo imaging
This project describes the construction of a 27 cm diameter, 50 cm long homogeneous Halbach array magnet. It consists of 23 rings, each with two layers of 12x12x12 permanent magnets. Design files are provided for those wanting to laser cut, CNC mill, or water-jet cut the positions of the magnets.…
ThinWire – MRI Gradient Coil Design
MATLAB tool to design simple geometry gradient coils
Software application and development platform for medical image visualization, analysis, quantification, segmentation, and registration. Supports all imaging modalities, wide range of data types (surface and volumetric meshes, textured surface scans, spectrum data, points, lines, curves, tables, etc.),…
This GPA originated from a collaboration with Jason Stockmann (MGH Harvard). The device can drive up to 4 channels with max 10 A. It is controlled via a single SPI galvanically isolated connection that is also used to read information from the current sensors. Sample code for an Arduino is given that…
The hMRI-toolbox is an easy-to-use open-source and flexible tool, for qMRI data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation),…
Anser EMT – the first open-source electromagnetic tracking platform for image-guided interventions
The Anser project provides an open-source implementation for electromagnetic tracking (EMT) with particular application to image-guided interventions. This work provides implementation schematics for an EMT system which relies on low-cost acquisition and demodulation techniques using both National…
Water/Fat Separated MR Thermometry
QMRITools – Mathematica Toolbox for quantitative MRI data
QMRITools is written in Mathematica using Wolfram Workbench and Eclipse and contains a collection of tools and functions for processing quantitative MRI data.
MRILab – GPU accelerated MRI simulator
An efficient and versatile numerical MRI simulator with GPU parallel acceleration
Gradient Coil Design
A repository that contains many Matlab scripts used to design gradient MR coils.
The Michigan Image Reconstruction Toolbox (MIRT) is a collection of open source algorithms for image reconstruction (and related imaging problems) written in Mathwork’s MATLAB language.
32-channel RF receive chain amplifiers
This modular system provides bias tees for first stage RF preamplifiers, second stage amplification, and programmable attenuation for use in MR scanners and other RF signal applications (at least up to several hundred MHz). Accommodates 32 channels and can be extended by daisy-chaining additional…
PyPPM – A proton precession magnetometer
Hardware and software designs that enable performing Nuclear Magnetic Resonance experiments using the Earth’s magnetic field.
Pulseq-GPI / IMR-framework
Python-based and UI-based pulse sequence design.
OCRA – Open Source Console for Real-Time Acquisition
OCRA stands for Open-source Console for Real-time Acquisition. It is a low-cost, open-source console (hardware controller) for MRI. Conventional MRI consoles may be high cost, closed-source, and inflexible, in that it is not possible to change acquisition parameters once the scan is started. In contrast,…
Structured-light 3D scanner
A 3D Scanner based on structured light and stereo vision.
OpenICE – Medical device interoperability platform
OpenICE is an initiative to create a community implementation of an Integrated Clinical Environment. The initiative encompasses not only software implementation but also an architecture for a wider clinical ecosystem to enable new avenues of clinical research. OpenICE seeks to integrate an inclusive…
ScopeFun – Several lab instruments in one device
Oscilloscope, Waveform Generator, Spectrum Analyzer, Logic Analyzer and Pattern Generator in one device.
Spinal Cord Toolbox – Image processing for multiparametric MRI
Spinal Cord Toolbox is a comprehensive software for the processing and analysis of multiparametric MRI data of the spinal cord.
Instructional tabletop MRI scanner
The scanner design is a low-cost resource for demonstrating concepts like magnetic resonance, spatial encoding, and the Fourier transform in an educational setting. A significant part of the system design is open-source.
qMRLab – Quantitative MRI under one umbrella
An open-source software for quantitative MR image analysis.
Blind Source Separation of Diffusion MRI
A diffusion model-free framework with echo time dependence for free-water elimination and brain tissue microstructure characterization.
Direct signal control – Optimal B1+ parallel transmission framework
Direct signal control provides reduced transmision field inhomogeneity allowing to recover regions of low signal without increasing imaging time or interecho spacing.
Quantitative Magnetization Transfer MRI Optimization Toolbox
This toolbox optimizes the acquisition protocols for spoiled gradient echo qMT sensitivity against noise and also sensitivity-regularization for robustness of a qMT parameter-of-interest.
High dynamic range processing for local contrast-enhancement in MRI
A high dynamic range image processing algorithm which can offer enhanced contrast and feature preservation for multichannel and multisequence MRI.
Ultimate intrinsic SNR in a uniform sphere
This program allows to calculate the ultimate intrinsic SNR at the center of a uniform dielectric sphere, which may be used, for example, as an absolute reference to assess the performance of head coils with spherical phantoms.
Hybrid MRI‐Ultrasound scannerless real‐time imaging
This project proposes a hybrid system based on a single‐element ultrasound transducer and an MR scanner to help boost temporal resolution in real‐time MRI.
SequenceTree – Pulse sequence programming in a dynamic visual environment
A user friendly software environment for implementing MRI pulse sequences and, exporting them to actual MRI scanners.
Pneumatic Phantom for Mimicking Respiration-Induced MRI Artifacts
An MRI compatible phantom that simulates the respiration of a human subject in an automated way. A pressure probe is used in order to communicate in continuous time to Matlab the evolution of the respiratory cycle of the subject.
TOPPE – Rapid MR pulse sequence prototyping
TOPPE is a simple, modular framework for rapid prototyping of pulse sequences on General Electric MRI scanners.
FID-A – Advanced MR spectroscopy processing and simulation
Advanced toolbox for design and analysis of radiofrequency (RF) pulses, and processing of magnetic resonance spectroscopy data.
High Peak/Average Power TR-Switch for Thermal MR
A high‐performance Tx/Rx switch design is presented that supports high peak and high average power applications such as MR imaging, RF heating or thermal MR.
Syringe Pump Library
Customizable high-quality syringe pumps
R-project – Statistical computing
R is a state-of-the-art statistical computing software with powerful graphic possibilities.
ODIN – Object-Oriented Development Interface for NMR
ODIN is a C++ software framework to develop and simulate magnetic resonance sequences.
GNU Octave – Scientific programming language
GNU Octave is a high-level language, primarily intended for numerical computations.
Open fMRI – Sharing brain MRI data
OpenfMRI.org is a project dedicated to the free and open sharing of raw MRI datasets.
Spinach – Simulating spin dynamics
Spinach is software library for simulation of spin dynamics in large spin systems. It supports NMR, EPR, DNP, MAS, PHIP, singlet state NMR and other forms of Magnetic Resonance spectroscopy.
EEZ H24005 – Bench Power Supply
EEZ H24005 is a power supply that provides features of middle and high range commercial devices.
FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data
OpenBCI – Open-source EEG
Open-source brain-computer interface (OpenBCI) is an affordable bio-sensing system that can sample electrical activity of human body such as brain (EEG), skeletal muscle (EMG) and heart (ECG) activity.
OPENCORE NMR is an open-source toolkit for implementing an NMR spectrometer. This console has the size of a laptop computer, making it easy to transport. The cost of its parts is very low compared to the prize of commercial systems.
Gadgetron is an open source framework for medical image reconstruction. It consists of two main components: First, a modular, high performance framework for streaming data processing through a set of modules or “Gadgets”. Second, it provides a set of tool-boxes for common image reconstruction…
gpuNUFFT – GPU based fast image reconstruction
gpuNUFFT is an open-source GPU Library for reducing computational time of non-linearly sampled 3D/2D MRI data with direct Matlab interface.
Berkeley Advanced Reconstruction Toolbox (BART)
The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays,…
PowerGrid is an accelerated, open source, freely available toolkit for iterative reconstruction supporting non-Cartesian trajectories. Using high level compiler directives, GPU accelerated Fourier transform operators were implemented in a high level syntax designed to correlate with the popular Image…
openEMS – A free and open electromagnetic field solver
openEMS is a free and open electromagnetic field solver using the FDTD method. Matlab or Octave are used as an easy and flexible scripting interface.
Pulseq – Open-source pulse sequences
Open Source framework for the development and hardware-independent execution of MR pulse sequences for imaging and spectroscopy. MRI sequences can be programmed in MATLAB and executed on real hardware.
Current Driver for Local B0-Shim Coils
Low cost, open source, scalable, current feedback controlled coil driver circuit for matrix B0 shim coils and related applications.
NMR Relaxometry Platform
Low cost, open source hardware platform for use in NMR relaxometry experiments. The platform is capable of a wide variety of relaxometry experiments comprising many magnet, coil, and sample combinations.
Open Source MRI sequence development and simulation environment
MARIE – Magnetic Resonance Integral Equation Suite
A prototype MATLAB open source software for the fast electromagnetic analysis of MRI systems.
COSI Measure is an open source multipurpose 3-axis robotic system that allows submillimeter movements for applications such as static/dynamic field mapping, CNC machinery or 3D printing.