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What's New

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

[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 is capable of serving as a mainstream scientific-data interchange format in the future, and fulfills part of the roles achieved by HDF5.

JSONlab is my attempt of adding JSON support in MATLAB. It contains loadjson.m - a JSON->MATLAB decoder, and savejson.m - a MATLAB->JSON encoder. I tested the script with a number of complex JSON inputs, and it worked fine! If you want to test the working script, you can download it from the subversion.

[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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