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What's New

(this site is currently under construction, new resources and links are being added constantly)

[April 27 2011] New grant award from Mass Life Science Center

I feel extremely lucky to be one of two persons that received this year's Cooperative Research Matching Grants from the Mass. Life Science Center. Here is the official press-release announced today, and an interview by Mass High Tech News this morning. I truly grateful for the support from MLSC, and looking forward to the exciting new project.

[April 19 2011] Comment on comparisons of mesh-based Monte Carlo software

A letter article came out today on BOE, commenting on a recent comparison study for mesh-based MC. We found that the discussions on computational speed and conclusions are questionable. We also found differences in RNG settings, Russian rulluttee settings and memory utility. Here is the author's reply. Please also note that TIM-OS and other MCML-inspired software imposes specular reflection while MMC doesn't. See this FAQ. A new version of MMC (v0.8) is expected to be released soon.

[March 31 2011] Digimouse atlas FEM mesh

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.

[March 20 2011] Announcing MCX and MCXLAB v0.5.0

It is my great pleasure to announce the final release of MCX v0.5. The most important addition in this release is MCXLAB, the native MEX version of MCX for MATLAB and GNU Octave. Now you can do everything, including setting up the problem domain, launching simulations and analyzing the results, entirely inside MATLAB/Octave without involving disk files. Here are some screenshots for MCXLAB in MATLAB and Octave. For more details, please read the Full Release Notes and ChangeLogs. Download the software from this page.

[February 28 2011] Release announcement for iso2mesh 1.0

The most important release yet of the iso2mesh toolbox, i.e. version 1.0, has finally arrived! Please read the Release notes and ChangeLogs to find more details. This is a stable release and is highly recommended to install or upgrade.

[February 05 2011] Making an anatomically accurate digital brain FEM mesh

Happy Chinese new year! At the beginning of the Rabbit year, 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 a "narrative" Release Notes.

[January 31 2011] Release candidate for iso2mesh 1.0

The release candidate of iso2mesh 1.0 (i.e. v0.9.9) is now available for download. Please read the release note, full ChangeLog and SVN commit history to learn more details.

[December 21 2010] Radiology paper is on the front cover!

Just found out today when seeing a copy in the mail. Our paper is on the front cover of the Jan 2011 issue of Radiology. The cover scan is on the right :)

[December 15 2010] MMC second release is announced

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. Just for fun, I also got it working on my Epic, see this screenshot for a proof :)

[November 09 2010] Press release from RSNA

A new paper on combining optical and x-ray mammography was recently accepted by Radiology. Here is the press release from RSNA. The paper preview is also published on Radiology's website. Here is the CBS news and report of this work (Dr. Kopans is the clinical collaborator on this project).

[November 03 2010] MMC first release is announced

A new open-source software, Mesh-based Monte Carlo (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. Download it from here.

[September 10 2010] Slides on MCX and MMC

Here you can find my slides presented at the 2010 Virtual Photonics Workshop at BLI. It was a wonderful event organized by Dr. Venugopalan and Dr. Spanier.

[August 01 2010] MCX v0.4.9 is released

It is my great pleasure to announce the availability of a new beta release, v0.4.9, of Monte Carlo eXtreme (MCX) - a GPU-accelerated Monte Carlo 3D photon transport simulator (URL: http://mcx.sf.net). Please read the release notes and the detailed Change Log/SVN history. The pre-compiled binaries for Linux/Windows can be accessed via the download page.

[July 25 2010] Collins adult brain atlas FEM mesh for download

I would like to share the human brain atlas FEM mesh I generated for a recent paper to researchers in the fields of neoroscience and imaging. The mesh data is now released in the public domain. You can download it from this page. The mesh contains 69865 nodes, 425224 tetrahedral elements and 4 tissue types. The "Sphere-Diffusion" toolbox is also available for download.

[July 22 2010] Image Guided Spectroscopy Symposium

Just returned from a wonderful symposium organized by Dartmouth NIRFAST team. I presented iso2mesh as an open-source meshing option. You can download my slides from here (PDF, 4.6MB).

[July 16 2010] Prior-guided image reconstruction

Just one day later, another paper submitted to Biomedical Optics Express was also published online(PDF, HTML). In this paper, we report a structural-prior-guided image reconstruction algorithm, combining a gray-scale tissue anatomy in a diffuse optical imaging reconstruction to improve image resolution and robustness.

[July 15 2010] Mesh-based Monte Carlo

A paper on a mesh-based Monte Carlo algorithm was accepted by Biomedical Optics Express and published online (PDF,HTML) today. The HTML-formatted full-text of the paper looks awesome. Glad to see that MathML is used to display all the equations!

The software will be released in the next a few days at MMC homepage at http://mcx.sourceforge.net/mmc/ after a few more touches to the documentation.

[July 14 2010] iso2mesh toolbox 1.0beta is released

Iso2mesh 1.0-beta (aka 0.9.8) is now released! It has been over a year since the previous release and the new software contains numerous updates and additions. Please download the new version from this page.

[June 06 2010] Converting a closed surface to a volumetric image

A missing link, surf2vol, in the iso2mesh roadmap is finally added. This may enable a number of new path-ways as the meshing pipeline is now a close-circuit. A possible one would be to remove self-intersecting elements by remeshing the surf2vol output.

[May 30 2010] Matlab Toolbox for the Analytical Diffusion/Helmholtz Solutions of a Sphere

The "Sphere-Diffusion" toolbox solves for the analytical solutions for the diffusion inside and outside a sphere. The solutions are defined in the 3D space on a user specified grid; the sphere can have different absorption/scattering/refractive index to the background media. This toolbox can be useful when evaluating new algorithms in the heterogeneous media.

You can find more details by clicking this link.

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