What's New
(this site is currently under construction, new resources and links are being added constantly)
[January 19 2012] Monte Carlo eXtreme new stable and beta releases
Happy new year! I am excited to let you know that two new releases for MCX and MCXLAB had become available recently. In the stable release v0.5.3, we fixed a forward-scattering-bias issue, discovered by David Giraud from BU, and added JSON-formatted input file support. In the beta release v0.7.9, we added additional support for 3D shape files and run-time rasterization. You are recommended to upgrade to the news releases. Your feedback to the new beta release is welcome! See ChangeLogs for more details. Get them from here.
[December 20 2011] Mesh-based Monte Carlo 0.9.0
MMC v0.9.0 has arrived with many bug fixes and new features! Thanks to a patch contributed by my colleague
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.
I would also make a preannouncement to the next milestone release of MMC, i.e. version 1.0. We will include wide-field illumination and MPI supports in MMC, as a result of a collaboration between me and Dr. Xavier Intes and Jin Chen from RPI (Jin did excellent job implementing this). Stay tuned if you are interested.
[November 13 2011] Postdoc opening at MGH/Harvard (Update: Position filled, 02/09/2012)
I am looking for a postdoctoral research fellow as part of a new collaboration with Philips Healthcare (Andover, MA) on developing novel multimodality breast imaging systems. The job description is detailed in this link. If you are interested, please email me your research statement, full CV, at least 2 recommendation letters or list of references.
[October 11 2011] JSON encoder and decoder and JMesh specification
JSON (JavaScript Object Notation) is a highly portable, human-readable and
"fat-free" text
format to represent complex and hierarchical data. It is as powerful as XML, but less
verbose. It is my opinion that JSON has the potential of serving as a mainstream scientific-data interchange
format in the future, and fulfills part of the roles achieved by
HDF5.
JSONlab is a by-product of my
effort in developing a flexible mesh description file format (.jmesh) for my mesh generator.
It contains loadjson.m - a JSON->MATLAB decoder, and
savejson.m
- a MATLAB->JSON encoder. The loadjson.m script was derived from the previous works
by several other people. I tested the script with a number of
complex JSON inputs,
and it worked just fine! If you want to try out this toolbox, you can
download it from its subversion.
- Update [2012/01/14]: JSONlab 0.8 is announced, and it gets a new logo! It is 20x faster when loading large arrays in MATLAB. Download it from here. Thanks to Mykel Kochenderfer@Lincoln Lab for many useful feedbacks!
- Update [2011/10/16]: the first JSONlab release is available for download.
[September 21 2011] Bug fix in MCX 0.5.2
I just announced a new release of MCX,
version 0.5.2, in the MCX mailing list. In this release, I fixed a bug related to using non-integer detector positions for mcx_det/mcx_det_cached, a bug reported by my colleagues at
Ecole Polytechnique Montreal. It also contains
a few improvements. If you use "detective MCX" in your research to calculate partial pathlengths, I urge you to update the software to the
latest version.
[September 3 2011] New Project Announcement: Blit
It is my pleasure to share another new project with you.
Blit is an open-source library for ``block iterative sparse linear solvers''. I will implement the
block versions of QMR, GMRES and CG algorithms to speed-up model-based medical imaging computation where solutions at multiple source/detector locations are required. Currently, BLQMR algorithm has been successfully implemented in MATLAB and FORTRAN90. A C/C++ header unit will be added soon. You can access the latest code from the
git repository at Sourceforge. Please browse Blit's homepage at
http://blit.sf.net for more details.
[August 9 2011] MMCM paper ranks 9th in BOE July downloads
The
mesh-based Monte Carlo method (MMCM) paper published last year enters the
top download list of
Biomed. Optics Express (BOE) in July.
[June 17 2011] Milestone release for MMC and new update for MCX
Mesh-based Monte Carlo (MMC) version
0.8.0 is a milestone release. It contains numerous updates including important new features and critical bug fixes. The software had been thoroughly validated and optimized for better speed. The highlights of the new release include 3 new ray-tracing algorithms, SSE accelerated computation, partial path-length recording and fixing critical bugs in mesh file generation. You can find more in the
Release Notes and
full ChangeLogs. Get it from
this link.
The GPU-based Monte Carlo simulator, MCX, also received a new update, v0.5.1, last week. It contains a fix to the shared memory buffer and improved flux/fluence normalization. MCXLAB was also updated to 0.5.1. Find more from the Release Notes and download the updated software from here.
[June 4 2011] Iso2mesh v1.0.1
Iso2mesh v1.0.1 is a maintenance release, it fixed several bugs and issues in the 1.0 version and added 64bit binary support and integrated CGAL polyhedral mesher. See
Release note and
ChangeLogs. Download it from
here.
[April 28 2011] Grand challenges explorations award from the Gates Foundation
Today, the
Gates Foundation announced the
wining applications for the Round 6 of
Grand Challenges Explorations grants, including a grant proposal of mine (#3 in the
list). I will be developing ultra-portable and
low-cost cell-phone based imaging application.
[April 27 2011] New grant award from Mass Life Science Center
I feel extremely honored to be one of the two awardees receiving the highly-competitive
Cooperative Research Matching Grants (Round 2) from the
Mass. Life Science Center. Here is the official
press-release announced today, and
an interview by
Mass High Tech News. I am truly grateful for the support from MLSC and Philips, and looking forward to the exciting new project.
Update 05/04/2011: Interview by Health Imaging News, thanks to Clint vanSonnenberg.
[April 19 2011] Comment on comparisons of mesh-based Monte Carlo software
A
letter came out today on
BOE, commenting on a recent
comparison study for mesh-based MC. In the original article, the discussions on computational speed and the main conclusion were found questionable. We also found differences in random-number-generator settings, Russian roulette settings and memory utility. Here is
the author's reply. Please also note that MCML-inspired software (CUDAMCML, TIM-OS etc) 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 receiving 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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