Mesh-based Monte Carlo (MMC)

Monte Carlo photon migration in complex shapes using volumetric meshes

• Mesh-based Monte Carlo, or MMC, is a Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MCX or tMCimg), MMC can represent a complex domain using a volumetric mesh. This not only greatly improves the accuracy of the solutions when modeling objects with curved/complex boundaries, but also gives an efficient way to sample the problem domain and uses less memory. The current version of MMC supports multi-threading and SIMD features on modern multi-core CPUs.
• MMC is an open-source software developed by Qianqian Fang who is an Assistant Professor at the Dept. of Bioengineering of the Northeastern University.
• Details of this software can be found in the following paper:
  • Qianqian Fang, "Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates," Biomed. Opt. Express 1(1), 165-175 (2010)
  • Qianqian Fang and David R. Kaeli, "Accelerating mesh-based Monte Carlo method on modern CPU architectures ," Biomed. Opt. Express 3(12), 3223-3230 (2012)
  • (NEW!) Ruoyang Yao, Xavier Intes, Qianqian Fang, "Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation," Biomed. Optics Express, 7(1), 171-184 (2016)

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Additional free software and data

• MMCLAB: a Matlab/Octave toolbox for mesh-based Monte Carlo (Version 0.9.5-1, released on 01/05/2014)
• Colin27 adult brain atlas FEM mesh (Version 2, released on 02/05/2011)
• Digimouse atlas FEM mesh (Version 1, released on 03/31/2011)
• Matlab Toolbox for the Analytical Diffusion/Helmholtz Solutions of a Sphere (Version 1.0.0)

What's New

• [2016/01/01] Happy new year! We are thrilled to kick off Year 2016 by presenting you a brand new release of MMC - 2016.1 (v1.0-beta)! This new release brings you complex wide-field sources support, MMCLAB for 64bit Windows and tons of bug fixes, results of two-year continuous improvement of the software. We are also excited to let you know, our paper regarding the new algorithm behind this new release has been published online on the Biomed. Optics Express's website. Please take a look at our paper, download the latest software, and enjoy the new and enhanced MMC simulation experience!
• [2015/12/11] We are glad to announce a preview for a new lease (1.0 beta) of MMC. A key feature added to this new release is the support of complex illumination and detection strategies. Over 10 different source types are now supported, including SFDI patterns, isotropic sources, cone beams, Gaussian beams etc. All area beams allow to be convergent or divergent. The latest software source code has been continuously developed through our MMC portal on Github under the "widefield" code branch. A new release and publication are expected in the next few weeks.
• [2015/06/08] It is my great pleasure to announce that, the MCX/MMC Monte Carlo simulation platform has received a 4-year funding support from NIH (National Institute of Health)/NIGMS (National Institute of General Medical Sciences) starting this summer! This marks a new chapter for MCX/MMC development. In this new project, I will be working with a number of leading experts, Dr. Simon Arridge (UCL), Dr. David Kaeli (Northeastern) and Dr. Xavier Intes (RPI), on advancing MCX/MMC towards one of the fastest, most comprehensive and accurate photon transport simulator. We will develop rapid computational models not just for forward modeling, but also for rapid image reconstructions; we have also proposed new methods to further speed up simulation by 10x or more. In addition, we plan to organize workshops, share detailed training materials and write intuitive user interfaces to make MCX/MMC even more easy-to-use. A detailed workplan will be posted shortly. I am looking forward to serving this growing community, and meeting everyone in one of our future events!

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