The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation.

The siemens_to_ismrmrd converter is used to convert data from Siemens raw data format into ISMRMRD raw data format.

This package provides a Python library for manipulating data saved as ISMRMRD.

Plastimatch is a computer software application which has been designed for volumetric (usually medical) image processing and radiation therapy applications. It can be used for the following purposes:

• Deformable registration

• Atlas-based segmentation

• Image conversion and manipulation

• Vector field conversion and manipulation

• Gamma analysis

• Dose calculation

• Registration analysis (Jacobian)

• Segmentation analysis (Dice, Hausdorff)

A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. The ISMRMRD project describes such a common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. This package provides a C/C++ library for working with the format.

STIR is an object-oriented framework for tomographic image reconstruction, with an emphasis on iterative reconstruction in PET and SPECT. This package includes the C++ core and Python bindings.

This package provides a hash table library that offers dynamicaly resizing tables and arbitrary number of hash keys insert and queries.

libspatialindex provides spatial indexing utilities, with support for sophisticated spatial queries and interfaces for updating information and customizing the storage management of indices. The library is written in C++, with a C API.

Medit was developped to visualize numerical simulation results on unstructured meshes in two and three dimensions. Scalar, vector and tensor fields can be easily associated and displayed with meshes.

libsupermesh is a Fortran 2008 library to intersect two overlapping meshes element by element. Pairs of overlapping elements are identified and a local mesh of their intersection is generated.

Approximate convex decomposition enables efficient geometry processing algorithms specifically designed for convex shapes (e.g., collision detection). We propose a method that is better to preserve collision conditions of the input shape with fewer components. It thus supports delicate and efficient object interaction in downstream applications.

The purpose of the GMlib is to provide programmers of solvers or automated meshers in the field of scientific computing with an easy, fast and transparent way to port their codes on GPUs (Graphic Processing Units).

This library is based on the OpenCL language standard, thus taking advantage of almost every architectures supported by most platforms (Linux, macOS, Windows).

It is a simple loop parallelization scheme (known as kernels in the realm of GPU computing), provides the programer with pre defined mesh data structures, automatically vectorizes unstructured data like the ball of points or the edge shells, and handles transparently the transfer and vectorization of mesh data structures.

The Gamma Mesh Format (GMF) and the associated library libMeshb provide programers of simulation and meshing software with an easy way to store their meshes and physical solutions. The GMF features more than 200 kinds of data types, like vertex, polyhedron, normal vector or vector solution field. The libMeshb provides a convenient way to move data between those files, via keyword tags, and the user's own structures.

The purpose of the LPlib is to provide programmers of solvers or automated meshers in the field of scientific computing with an easy, fast and transparent way to parallelize their codes. This library is based on posix standard threads, also known as pthreads, thus taking advantage of multi-core chips and shared memory architectures supported by most platforms (Linux, macOS, Windows).

Version 4 provides an early implementation of colored grains scheduling for better scaling and memory localization with high core count systems.

The libOL first store a mesh made of vertices, edges and triangles in an octree structure with a very small memory footprint. Subsequently, you can perform geometrical queries very quickly on this mesh:

• retrieve the closest entity from a given set of coordinates

• build the list of mesh entities than are include in a given bounding box

• project a vertex on any kind of geometrical entity

• launch a ray and get the first intersected entity

• all query operations can be performed in parallel as the library is thread safe

This package contains the binary resulting from the compilation of hello_c.c in the examples subdirectory of the Open MPI source code. It can be used to check MPI connectivity on a machine/cluster.

MVAPICH2 (pronounced as “em-vah-pich 2”) is an open-source MPI software to exploit the novel features and mechanisms of high-performance networking technologies (InfiniBand, iWARP, RDMA over Converged Enhanced Ethernet (RoCE v1 and v2), Slingshot 10, and Rockport Networks) and deliver best performance and scalability to MPI applications.

MVAPICH (pronounced as “em-vah-pich”) is an open-source MPI software to exploit the novel features and mechanisms of high-performance networking technologies (InfiniBand, iWARP, RDMA over Converged Enhanced Ethernet (RoCE v1 and v2), Slingshot 10, and Rockport Networks) and deliver best performance and scalability to MPI applications. MVAPICH 4.1 has support for the Cray Slingshot 11, Cornelis OPX, and Intel PSM3 interconnects through the OFI libfabric library, and for the UCX communication library.

Umpire is a resource management library that allows the discovery, provision, and management of memory on machines with multiple memory devices like NUMA and GPUs.

The PETPVC toolbox comprises a suite of methods, both classic and more recent approaches, for the purposes of applying PVC to PET data. Eight core PVC techniques are available, and those core methods can be combined to create a total of 22 different PVC techniques.

Convert data from DICOM and organise the resulting NIfTI files into BIDS.

This package provides programs to perform EM based segmentation of images in nifti or analyse format.

NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data, designed and optimized for human infants between 0-2 years old.

Nipype provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages.