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             Monte Carlo eXtreme (MCX) Suite
                    version 2023
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Copyright (c) 2009-2023  Qianqian Fang <q.fang at neu.edu>

- Computational Optics & Translational Imaging (COTI) Lab (http://fanglab.org)
- Department of Bioengineering, Northeastern University
- 360 Huntington Ave, ISEC 206, Boston, MA 02115, USA
- Website: http://mcx.space
- Github: https://github.com/fangq/mcx/

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:: 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)

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:: 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.

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:: 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 ===

[Yan2022] Shijie Yan, Steven L. Jacques, Jessica C. Ramella-Roman, Qianqian Fang, "Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media," J. of Biomedical Optics, 27(8), 083015 (2022)
*Summary: Polarization-enabled MCX
*Download: https://doi.org/10.1117/1.JBO.27.8.083015

[Fang2022] Qianqian Fang, Shijie Yan, "MCX Cloud—a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing," J. Biomed. Opt. 27(8) 083008, 2022
*Summary: MCX Cloud
*Download: https://doi.org/10.1117/1.JBO.27.8.083008

[Yan2020b] Shijie Yan and Qianqian Fang* (2020), "Hybrid mesh and voxel based Monte Carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues," Biomed. Opt. Express, 11(11) pp. 6262-6270.
*Summary: Hybrid voxel/mesh based MC - SVMC
*Download: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-11-11-6262

[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 ===

[Zhang2022] Yuxuang Zhang, Qianqian Fang, "BlenderPhotonics – an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues," J. of Biomedical Optics, 27(8), 083014 (2022)
*Summary: BlenderPhotonics
*Download: https://doi.org/10.1117/1.JBO.27.8.083014

[Yuan2021] Yaoshen Yuan, Shijie Yan, and Qianqian Fang*, "Light transport modeling in highly complex tissues using the implicit mesh-based Monte Carlo algorithm," Biomed. Optics Express, 12(1), 147-161, (2021)
*Summary:  Implicit MMC (iMMC)
*Download: https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147

[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 ===

[Hirvi2023] Hirvi P, Kuutela T, Fang Q, Hannukainen A, Hyvonen N, Nissilä I. Effects of atlas-based anatomy on modelled light transport in the neonatal head. Phys Med Biol. 2023 May 11. doi: 10.1088/1361-6560/acd48c. PMID: 37167982.
*Summary: RF replay and neonatal brain atlas
*Download: https://doi.org/10.1088/1361-6560/acd48c

[RaayaiArdakani2022] Matin Raayai Ardakani, Leiming Yu, David R. Kaeli, Qianqian Fang, "Framework for Denoising Monte Carlo Photon Transport Simulations Using Deep Learning," J Biomed Opt. 2022 May;27(8):083019. doi: 10.1117/1.JBO.27.8.083019
*Summary: DL-based MC denoising
*Download: https://doi.org/10.1117/1.jbo.27.8.083019

[Dumont2021] Dumont, A.P., Fang, Q. and Patil, C.A., "A Computationally Efficient Monte‐Carlo Model for Biomedical Raman Spectroscopy," J. Biophotonics, (in press), (2021)
*Summary: Raman MCX
*Download: https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202000377

[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

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