What's New
(this site is currently under construction, new resources and links are being added constantly)
[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.
[May 14 2010] MCX benchmarked on GTX 470
MCX was recently benchmarked on a
GTX 470 card and had achieved a speed of 12800 photons/millisecond using over 40000 threads and a block size of 512. This is 4x faster than the
results with 8800GT.
[May 10 2010] New demo added to iso2mesh
iso2mesh now supports mesh refinement by exploiting the existing features from
tetgen (thanks to
Hang Si, the author of tetgen). See
this page for a demo (the demo also shows how to create spheres from iso2mesh). Please
check out the latest code from SVN to give it a try.
[Apr 11 2010] OSA talks
Slides for the two talks at
OSA BIOMED conference (warning: all the GIF and ppt animations are not available in the PDF file):
[Feb 13 2010] Chinese new year (year of tiger)
With the recently implemented JSONP support in the Habitat engine, I was finally able to build a "live" research homepage from the read-only center web space . Some of the "old" news in the past year are posted below.
[Jan 26 2010] GPU Ocelot support added to MCX
Ocelot is an open-source PTX emulator developed by Greg Diamos and his colleagues. A makefile is added to MCX SVN to enable linking against libocelot and execution on CPU. Unfortunately, Ocelot emulation is very slow, this is expected to be improved significantly by the coming PTX-LLVM translator.
[Dec 22 2009] MCX 0.2 final is released
The GPU-accelerated open-source Monte Carlo simulation software, Monte Carlo eXtreme (MCX), v0.2 final is now released. Pre-compiled binaries for multiple platforms as well as the full source code can be downloaded from here. The major updates include an addition of a cross-platform GUI tool for MCX.
[Oct 21 2009] MCX 0.2 beta released with paper accessible online
Monte Carlo eXtreme (MCX), v0.2 beta, is released for Linux (32/64bit), Windows and Mac OS. The full paper describing this work is now a featured article on the Optics Express website.
[Jul 01 2009] iso2mesh work presented at IEEE ISBI
I presented a poster(PDF 2.5M) at ISBI'2009 and gave an introduction to the open-source iso2mesh 3D mesh generator. More details can be found in this short paper. Thanks to CGAL and a few other developers for their awesome software enabling this toolbox.