Qianqian Fang’s Post

View profile for Qianqian Fang

Department of Bioengineering…948 followers

Excited to announce the first public release of #Redbird - a comprehensive 3-D diffuse optics forward modeling and image reconstruction toolbox for #MATLAB and #GNUOctave. 📦 Download it from here neurojson.org/Page/Redbird Other researchers/students may get to know my group's works via our #MonteCarlo photon simulators -- #MCX and #MMC. However, I did spend a good amount of my time solving the diffusion equation (DE), inverse problems and prior-guided reconstructions. Redbird is the result of those countless hours. The development of #Redbird can be traced all the way back when I was a PhD student studying microwave tomography (MWT). At the time, I wrote most of the core algorithms as part of my PhD dissertation, including finite-element based forward model (not for diffusion equation but Helmholtz equation), Gauss-Newton based iterative reconstruction, regularization strategies, dual-mesh modeling, adjoint method, multi-spectral reconstruction ..., EXCEPT that everything was written in #FORTRAN90 .... During my postdoc training, I extended this code to diffuse optical tomography (DOT) and named it Redbird - "red" for near-infrared. In the following 10 years, I used it extensively in almost every of our breast DOT papers. Many of the new developments, including prior-guided reconstructions, multi-modal data fusion, multi-RHS linear solver etc were added to the software, but it is still in FORTRAN90. Make no mistake, I love #FORTRAN90! it is fast, simple, effective, and also modern. Sadly, I realized that younger students no longer have interests to learn it. In 2018, I decided to rewrite redbird-FORTRAN90 in the MATLAB/Octave language just so that my own students can use it effectively (and understand how it works). In the past few years, this MATLAB version of redbird was further developed to support widefield/complex sources and built the foundation for our widefield compressive DOT and target-adaptive DOT. As part of my breast DOT R01 (R01-CA204443) renewed last year, we are now sharing this extensively developed toolbox to the broader biophotonics community to benefit from our 20+ years of research in DOT, inverse problems and model-based image reconstruction methods. Redbird is easy to install and easy to use. It is 100x faster than GPU-accelerated MC. As long as the medium is diffusive, redbird can produce accurate forward solutions across thousands of source and detector pairs in just under a minute using a single CPU core. More importantly, the inverse solvers in redbird can no only be used to perform DOI/DOT data analyses for DE forward models, but also for MC based forward models. Using a combination of #redbird and #mcx and #mmc, one can perform bulk-optical property fitting, segmented/layered tissue optical property estimation and full image reconstruction in arbitrary 3-D media. Check out the built-in examples here https://lnkd.in/eENxtFVA

Nicholas Ross

University of Notre Dame…2K followers

9mo

Congrats! It's impressive to see your dedication and hard work on this project after so many years.

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Yasin Gourkani

Freelance783 followers

9mo

Impressive

Hanxue Gu

Duke Spark Initiative for AI…2K followers

9mo

Congrats Qianqian! 🎉

Zhiying Xie

University of Washington761 followers

9mo

Amazing work!

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