[MCX Announcement] 3 new packages available: pmmc, pyiso2mesh and Redbird

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Qianqian Fang

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Jul 8, 2025, 5:26:38 PMJul 8
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Dear MCX/MMC registered users,


It is my great pleasure to announce 3 (!!!) new software packages to our user communities:


1. pmmc - Python binding of MMC

Following the steps of supporting Python in our previously announced pmcx and pmcxcl modules, we have also ported mmc to Python. You can install it via pip install pmmc


2. pyiso2mesh - Python port of iso2mesh

MMC is deeply integrated with our widely used 3-D mesh generator, Iso2Mesh. In order to port MMC to Python, we have to also re-implement iso2mesh in Python - which is exactly what we did - now, iso2mesh's native Python re-implementation is available on PyPi as well, you can download it via pip install iso2mesh



3. Redbird - a comprehensive diffusion-equation based DOI/DOT forward and inverse modeling toolbox (for MATLAB/Octave)

Redbird has been our "internally-used" diffusion and DOT image reconstruction toolbox since the days when I was a PhD student - it is a result of over 20+ years of research in DOT image reconstruction algorithms, forward modeling, prior-guided reconstructions, widefield DOT systems, and is behind almost all of the DOT related papers my lab published in the past (including data analyses from clinical measurements). 

It was originally written in FORTRAN90 (derived from my PhD work), and I rewrote it for MATLAB/Octave in 2018 just so that my own students can do efficient DOT data analysis and also understand how it works. The code is very compact (5000 lines of vectorized matlab code, with 1300 lines of comments), highly portable, and easy to modify and understand.

Under the support of my breast R01 project renewed last year, we are excited to share this extensively developed toolbox to the broader community. The forward model of Redbird is a lot like MMC - except that it solves the DE instead of RTE, thus is 100x faster than GPU-based MMC/MCX, and the output has no stochastic noise. it has been extensively validated against our MC solvers to ensure it matches the gold-standard solutions in diffusive domains. One key feature we added is the ability to model widefield sources such as pattern/planar/disk sources. 

Redbird is fast, easy-to-use, fully open-source, and can run on any platform where MATLAB/Octave is supported. A technical manual detailing the rigorous mathematical models in the forward/inverse models in redbird can be found  at https://github.com/fangq/redbird/blob/master/doc/Redbird_manual.pdf 

We are currently working on a journal paper describing this work and a Python port. stay tuned!



In addition, we are working on making a new release of MCX/MMC - in this new release, we have added international language support (i18n) to MCX, see our previous announcement here

https://www.linkedin.com/feed/update/urn:li:activity:7335029243275313152/


give these new tools a try and let us know if find those useful!

cheers!


Qianqian

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