============================================================= Monte Carlo eXtreme (MCX) Suite version 2020 ============================================================= Copyright (c) 2010-2020 Qianqian Fang - Computational Optics & Translational Imaging (COTI) Lab (http://fanglab.org) - Department of Bioengineering, Northeastern University - 360 Huntington Ave, ISEC 204, Boston, MA 02115, USA - Website: http://mcx.space - Github: http://github.com/mcextreme/ ============================================================= :: Acknowledgement: The MCX Project is funded by the US National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS) under grant R01-GM114365 (PI: Qianqian Fang) ============================================================= :: License: This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License, as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. The full text of the software license can be found at https://www.gnu.org/licenses/gpl-3.0.en.html To continue installation, you must agree with the above license. ============================================================= :: Citation: The technical details of the software tools included in this package can be found in the below publications. If you use MCX/MMC/MCX-CL in your research, you agree to cite the relevant papers in your publications. === MCX === [Fang2009] Qianqian Fang and David Boas, "Monte Carlo Simulation of Photon Migration in 3D Turbid Media Accelerated by Graphics Processing Units," Opt. Express, vol. 17, issue 22, pp. 20178-20190 (2009). *Summary: original MCX paper *Download: http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178 === MCX-CL === [Yu2018] Leiming Yu, Fanny Nina-Paravecino, David Kaeli, Qianqian Fang, "Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms," J. Biomed. Opt. 23(1), 010504 (2018). *Summary: original MCX-CL (OpenCL) paper *Download: https://doi.org/10.1117/1.JBO.23.1.010504 === MMC === [Fang2019] Qianqian Fang*, Shijie Yan, "Graphics processing unit-accelerated mesh-based Monte Carlo photon transport simulations," J. of Biomedical Optics, 24(11), 115002 (2019) *Summary: GPU-based MMC *Download: http://dx.doi.org/10.1117/1.JBO.24.11.115002 [Yan2019] Shijie Yan, Anh Phong Tran, Qianqian Fang*, "A dual-grid mesh-based Monte Carlo algorithm for efficient photon transport simulations in complex 3-D media," J. of Biomedical Optics, 24(2), 020503 (2019). *Summary: Dual-grid MMC for faster and more accurate mesh-based simulations *Download: http://dx.doi.org/10.1117/1.JBO.24.2.020503 [Fang2012] Qianqian Fang and David R. Kaeli, "Accelerating mesh-based Monte Carlo method on modern CPU architectures ," Biomed. Opt. Express 3(12), 3223-3230 (2012) *Summary: SIMD MMC *Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223 [Fang2011] Qianqian Fang, "Comment on 'A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation'," Biomed. Opt. Express, vol. 2, issue 5, pp. 1258-1264, 2011. *Summary: MMC ray-tracing comparisons *Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-2-5-1258 [Fang2010] Qianqian Fang, "Mesh-based Monte Carlo method using fast ray-tracing in Plucker coordinates," Biomed. Opt. Express 1(1), 165-175 (2010) *Summary: original MMC paper *Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165 === General MC algorithm === [Yan2020] Shijie Yan, Ruoyang Yao, Xavier Intes, and Qianqian Fang*, "Accelerating Monte Carlo modeling of structured-light-based diffuse optical imaging via 'photon sharing'," Opt. Lett. 45, 2842-2845 (2020) *Summary: "Photon sharing" for simultaneous multi-pattern simulation *Download: https://www.biorxiv.org/content/10.1101/2020.02.16.951590v2 [Yao2018] Ruoyang Yao, Xavier Intes, Qianqian Fang*, "A direct approach to compute Jacobians for diffuse optical tomography using perturbation Monte Carlo-based photon 'replay'," Biomed. Optics Express 9(10), 4588-4603 (2018) *Summary: Building Jacobians with replay in MCX/MMC *Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-4588 [Yuan2018] Yaoshen Yuan, Leiming Yu, Zafer Dogan, Qianqian Fang, "Graphics processing units-accelerated adaptive nonlocal means filter for denoising three-dimensional Monte Carlo photon transport simulations," J. of Biomedical Optics, 23(12), 121618 (2018). *Summary: Denoising MC simulation using a noise-adaptive filter *Download: https://www.spiedigitallibrary.org/journalArticle/Download?fullDOI=10.1117%2F1.JBO.23.12.121618 [Yao2016] Ruoyang Yao, Xavier Intes, Qianqian Fang*, "Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation," Biomed. Optics Express, 7(1), 171-184, (2016) *Summary: Widefield MMC *Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171 === Applications === [Yuan2020] Yaoshen Yuan, Paolo Cassano, Matthew Pias, Qianqian Fang*, (2020) "Transcranial photobiomodulation with near-infrared light from childhood to elderliness: simulation of dosimetry,", Neurophotonics, 7(1), 015009 *Summary: PBM dosage over lifespan *Download: https://doi.org/10.1117/1.NPh.7.1.015009 [Brain2Mesh2020] Anh Phong Tran, Shijie Yan, Qianqian Fang*, (2020) "Improving model-based fNIRS analysis using mesh-based anatomical and light-transport models," Neurophotonics, 7(1), 015008 *Summary: Brain2Mesh - a one-liner for brain mesh generator (http://mcx.space/brain2mesh) *Download: https://doi.org/10.1117/1.NPh.7.1.015008 [Cassano2019] Cassano P+, Tran AP+, Katnani H, Bleier BS, Hamblin MR, Yuan Y, Fang Q*, (2019) "Selective photobiomodulation for emotion regulation: model-based dosimetry study," Neurophotonics 6(1) 015004, PMCID: PMC6366475 *Summary: Use MCX to systematically study transcranial or intranasal photobiomodulation (t-PBM/i-PBM) light dosage *Download: https://doi.org/10.1117/1.NPh.6.1.015004 =============================================================