MCX/MMC Suite - GPU-accelerated photon transport simulation platform

Monte Carlo eXtreme, or MCX, is an open-source Monte Carlo (MC) photon simulator for modeling light transport in 3D turbid media. The MCX/MMC Suite also contains mesh-based Monte Carlo (MMC) - an anatomically accurate 3D Monte Carlo (MC) simulator that can use a tetrahedral mesh to represent extremely complex tissue structures.

Both MCX and MMC supports graphics processing units (GPUs) and are capable of simulating thousands of photons simultaneously, making them among the fastest and most accurate photon modeling tools. Since their initial releases, the MCX Suite has become one of the most widely disseminated biophotonics modeling platforms, well-known for its high accuracy, high speed and versatility, as attested to by its over 27,000 downloads and nearly 1,000 citations from a large (2,400 registered users) world-wide user community. This rapidly expanding user community presents a diverse set of demands and a wide range of applications in the form of continuously evolving complex imaging domains and modalities. We are dedicated to serving this active and growing research community, and draw strong motivation from our extensive interactions with users, aiming to further expand the breadth, complexity, and efficiency of our simulation platform.

The development of MCX/MMC simulation platform is funded by the NIH/NIGMS under grant R01-GM114365.

Iso2Mesh - 3D image based mesh generation toolbox

Iso2Mesh is a MATLAB/Octave-based mesh generation toolbox, designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, working either independently or interacting with external free meshing utilities. Iso2Mesh toolbox can directly convert a 3D image stack, including binary, segmented or gray-scale images such as MRI or CT scans, into quality volumetric meshes. This makes it particularly suitable for multi-modality medical imaging data analysis and multi-physics modeling. Iso2Mesh is cross-platform and is compatible with both MATLAB and GNU Octave.

JSONLab - MATLAB JSON/UBJSON/MassagePack encoder/decoder

OpenJData - Future-proof scientific data format

Brain2mesh - One-liner brain mesh generator