XClose

UCL Centre for Medical Image Computing

Home
Menu

Resources

Since its launch in 2005 the UCL Centre for Medical Image Computing has generated a wealth of open source software.

Please find below a sample of our currently most popular packages (you can test some of them online using NiftyWeb service). Follow the links to each package for information specific to a package. Please also refer to the People section of our website if you are looking for packages created by a specific team of developers within our Centre.

BrainPainter is a tool for colouring brain images using any user-defined input. For each brain region it takes values from a 0-1 (or 0-max), and colours the brain regions according to these numbers. Numbers could represent biomarkers, levels of atrophy, or absolutely anything.
https://github.com/ucl-pond/brain-coloring

UCL Camino Diffusion MRI Toolkit
Camino is an open-source software toolkit for diffusion MRI processing. The toolkit implements standard techniques, such as diffusion tensor fitting, mapping fractional anisotropy and mean diffusivity, deterministic and probabilistic tractography. It also contains more specialized and cutting-edge techniques, such as Monte-Carlo diffusion simulation, multi-fibre and HARDI reconstruction techniques, multi-fibre PICo, compartment models, and axon density and diameter estimation.
http://camino.cs.ucl.ac.uk

Image Quality Transfer (IQT) aims to bridge the technological gap that exists between bespoke and expensive experimental systems such as the Human Connectome Project (HCP) scanner and accessible commercial clinical systems using machine learning (ML). The technique learns mappings from low quality (e.g. clinical) to high quality (e.g. experimental) images exploiting the similarity of images across subjects, regions, modalities, and scales: image macro- and meso-structure is highly predictive of sub-voxel content. The mapping may then operate directly on low-quality images to estimate the corresponding high-quality images, or serve as a prior in an otherwise ill-posed image-reconstruction routine.
https://github.com/ucl-mig/iqt

MISST - Microstructure Imaging Sequence Simulation ToolBox
Microstructure Imaging Sequence Simulation Toolbox (MISST) is a practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. Its key purpose is to provide a deep understanding of the restricted diffusion MRI signal for a wide range of realistic, fully flexible scanner acquisition protocols, in practical computational time.
http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.MISST

NifTK package
A suit containing image processing tools, biomarkers like BSI and viewers like NiftyView, NiftyMITK, NiftyIGI and the open source part of NiftyMIDAS. This repository is open sourced under BSD.
https://cmiclab.cs.ucl.ac.uk/CMIC/NifTK

http://niftk.org

NODDI (Practical in vivo neurite orientation dispersion and density imaging of the human brain) is a practical diffusion MRI technique for estimating the microstructural complexity of dendrites and axons in vivo on clinical MRI scanners.
https://www.nitrc.org/projects/noddi_toolbox

POSSUM (Physics-Oriented Simulated Scanner for Understanding MRI) is a software tool that produces realistic simulated MRI and FMRI images or time series. POSSUM is part of FSL (FMRIB's Software Library). POSSUM has an easy-to-use graphical user interface (GUI) and its component programs can also be run from the command line. POSSUM includes tools for the pulse sequence generation, signal generation, noise addition and image reconstruction.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/POSSUM

SNAPPY is part of the SnappySonic and can be used as an ultrasound acquisition simulator. The output from a tracking system (NDI or AruCo tags) is to select a frame of pre-recorded video to show. A suitable video of ultrasound data is included in the data directory, however the user can select a video of their choosing. The software and its use is described in the SnappySonic paper here (https://openresearchsoftware.metajnl.com/articles/10.5334/jors.289/0)
 

https://github.com/UCL/snappysonic/

The Spherical Mean Technique (SMT) is a clinically feasible method for microscopic diffusion anisotropy imaging. The purpose is to map microscopic features unconfounded by the effects of fibre crossings and orientation dispersion, which are ubiquitous in the brain. This technique requires only an off-the-shelf diffusion sequence with two (or more) b-shells achievable on any standard MRI scanner, thus facilitating its widespread use in neuroscience research and clinical neurology.
https://github.com/ekaden/smt

Subtype and Stage Inference (SuStaIn) infers disease subtypes and their progression patterns from cross-sectional datasets.
If you use this code, please cite: https://doi.org/10.1038/s41467-018-05892-0.

https://github.com/ucl-mig/PySustaln

You may also want to find more about the following:

STIR is open source software for tomographic image reconstruction [1]. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET and SPECT, but other application areas and imaging modalities can be added.
(http://stir.sourceforge.net/)
More on software developed by our colleagues at UCL Institute of Nuclear Medicine
https://www.ucl.ac.uk/nuclear-medicine/research/researchabstracts/opensourcesoftwarepackagesatinm

UCL XNAT Service is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. It facilitates management, archiving, sharing and analysing medical imaging data and associated files.
(https://www.ucl.ac.uk/isd/services/research-it/ucl-xnat-service)
More on the software services offered by our colleagues in the Medical Imaging Research Software Group here:
https://www.ucl.ac.uk/research-it-services/services/software-development/medical-imaging-research-software-group