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CMIC Software and Open Source Database

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CMIC Software and Open Source Database

CMIC is developing several software tools that will be of interest to the wider medical imaging community. Here we give a brief overview of our well established software packages such as TOAST and Camino and our rapidly advancing translational imaging platform NifTK.

In addition to software, we also provide access to the MIRIAD database. More information can be found here. 


NifTK - A translational imaging platform

NifTK is the name of our platform, combining NiftyReg, NiftySim, NiftyRec and NiftySeg via the viewer NiftyView.  The aim is to take the tools that CMIC develops, and apply them in a clinical context. If you have any questions about the NifTK platform, please contact our CMIC Software Manager Matt Clarkson. The following sections provide more detail:


NiftyReg logo - Efficient medical image registration

NiftyReg contains programs to perform rigid, affine and non-linear registration of medical images. Two versions of the algorithms are included, a CPU- and a GPU-based implementation. Further information about the method can be found here. Contributors include Marc Modat, Pankaj Daga and Sebastien Ourselin.

Download here



NiftySim is a solver for non-linear elastic or visco-elastic deformation. Two versions of the algorithms are included, a CPU- and a GPU-based implementation. Contributors include Zeike Taylor, Marc Modat, Lianghao Han, Stian Johnsen and Sebastien Ourselin

Download here



NiftyRec is a software package for fully 3D Stochastic Emission Tomographic Reconstruction. The package includes a Matlab Toolbox with inline documentation and a library for for C/C++ development. Computationally intensive tasks have a GPU implementation based on CUDA. Currently MLEM, OSEM, and OSL-MAPEM reconstruction algorithms are supported. Contributors include Stefano Pedamonte,  and Sebastien Ourselin.

Download here



NiftySeg is an open-source software package for image segmentation, bias field correction and cortical thickness estimation. Image segmentation is based on an Expectation-Maximisation algorithm with a Markov random field for local consistency and an improved sulci delineation enhancement. Cortical thickness is measured using a Laplacian based metric within a Lagrangian-Eulerian framework. Contributors include Jorge Cardoso, Marc Modat, Matt Clarkson and Sebastien Ourselin.


Download here



NiftyView is a cross platform graphical user interface, providing an entry point to the above packages, and in addition, many of the usual features you would find in any medical image viewer. NiftyView provides a working environment for our clinical collaborators, and research scientists. Contributors include Matt Clarkson, Gergely Zombori, Miklos Espak, John Hipwell, Steve Thompson and Sebastien Ourselin.


Independent Software Packages

In addition to the above platform, CMIC has developed:


TOAST is a software suite for image reconstruction in optical diffusion tomography (ODT). The toolbox consists of a set of MATLAB functions, both in the form of compiled mex files that link directly into the TOAST libraries, and Matlab scripts that perform high-level tasks in modelling, reconstruction and vis-ualisation. Contributors include Martin Schweiger and Simon Arridge.

Download here.



Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. Contributors include most of Danny Alexander's group. 

Download here



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