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)
Additional free software and data
- [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!
- [2014/01/05] MMC 0.9.5 (code name: Wasabi Peas) is finally released! This release is a result of over 2 years' continuous improvement of the MMC software (62 files changed, 3399 new lines and 363 lines of deletions). A number of important new features are added, including the additions of MMCLAB, perturbation MC support, fast Jacobian calculation etc. Details can be found in the MMC/ChangeLog. Please download the new version of MMC & MMCLAB from this page.
- [2012/09/27] A new paper entitled "Accelerating mesh-based Monte Carlo method on modern CPU architectures" by Fang & Kaeli was accepted for BOE. In this work, we compared contemporary ray-tracing techniques, aiming for faster and more accurate Monte Carlo modeling on modern CPU processors. The described techniques have been incorporated in the MMC v0.8 and newer releases. Download PDF here.
- [2012/08/27] A new paper entitled "Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography" by Chen, Fang & Intes was accepted for JBO. In this work, the MMC software was extended to support wide-field illumination. In addition, MPI-based parallel computing for distributed systems was also added. The widefield branch of the MMC code is currently developed in the Git repo. This branch will be heading the next milestone release, version 1.0, for MMC.
- [2012/08/20] MMCLAB, an easy-to-use Matlab/Octave toolbox with full MMC features, is announced for testers. Learn more from here.
- [2012/08/10] The original MMC paper moved to the top in the BOE Top Download list.
- [2012/01/20] A JSON file loading bug was reported and fixed. Only windows users are affected. Please update your Windows binaries to 0.9.1.
- [2011/12/20] MMC v0.9.0 has arrived with many bug fixes and new features! Thanks to a patch contributed by Dr. Stefan Carp, MMC can record momentum transfer for detected photons and makes itself useful in diffuse correlation spectroscopy (DCS) studies. Please browse the Release Notes and ChangeLogs pages for more details.
- [2011/06/17] We are pleased to announce a major update to MMC, i.e. version 0.8.0. In this milestone release, we added a number of important features, including saving partial-path-lengths and SSE4 support. Several critical bugs were fixed. Please read the Release Notes and full ChangeLogs for more details. Please consider updating to this release for better accuracy and efficiency. Download v0.8.0 from this link.
- [2011/03/31] We release a new mouse atlas FEM mesh based on the popular Digimouse atlas dataset. The new mesh contains 30% less nodes but with improved mesh quality and much balanced element sizes. Mesh generation script and optical properties of 21 tissue types are provided.
- [2011/02/05] A new digital brain atlas FEM mesh is released into the public domain. The new mesh features more anatomically accurate gray/white-matter and CSF tissue boundaries, and among others. The detailed mesh generation process, including the matlab script, is described in the Release Note.
- [2010/12/15] A new version of MMC, v0.4.0 (codenamed "Pecan Pie"), has just been released. See the release note and ChangeLog. The default binary of the new code is roughly 2x faster than the previous release. It also features a new random number generator and initial Doxygen support. An Android binary is also provided to demonstrate the portability.
- [2010/08/29] The first release of MMC was announced. MMC supports more accurate tissue boundaries, and multi-threaded parallel computing. Please find the release notes and the original paper to learn more.
- [2010/07/15] A paper on a mesh-based Monte Carlo algorithm was accepted by Biomedical Optics Express and published online (PDF,HTML) today.