   #[1]Monte Carlo eXtreme: GPU-based Monte Carlo Simulations

Papers

                1.1. [2]MCX

                1.2. [3]MCX-CL

                1.3. [4]MMC

                1.4. [5]General MC algorithm

                1.5. [6]Applications

   If you use MCX/MMC/MCX-CL in your research, we appreciate if you can
   cite our relevant papers in your publications.

1.1. 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: [7]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: [8]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:
       [9]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-11-11-626
       2

     * [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:
       [10]http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178

1.2. 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: [11]https://doi.org/10.1117/1.JBO.23.1.010504

1.3. 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: [12]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:
       [13]https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147

     * [Fang2019] Qianqian Fang* and Shijie Yan, “Graphics processing
       unit-accelerated mesh-based Monte Carlo photon transport
       simulations,” J. of Biomedical Optics, 24(11), 115002 (2019).
     * Summary: GPU-accelerated (OpenCL) MMC algorithm and software - MMCL
     * Download: [14]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: [15]http://dx.doi.org/10.1117/1.JBO.24.2.020503

     * [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:
       [16]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171

     * [Jin2012] Chen J, Fang Q, Intes X, “Mesh-based Monte Carlo method
       in time-domain widefield fluorescence molecular tomography,” J. of
       Biomedical Optics, 17(10), 106009 (2012).
     * Summary: Axis-aligned wide-field MMC algorithm for fluorescence
       molecular tomography
     * Download: [17]https://doi.org/10.1117/1.JBO.17.10.106009

     * [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:
       [18]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-322
       3

     * [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:
       [19]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 Plücker coordinates," Biomed. Opt. Express 1(1),
       165-175 (2010)
     * Summary: original MMC paper
     * Download:
       [20]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165

1.4. 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: [21]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: [22]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:
       [23]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 simulations of multiple
       patterns
     * Download:
       [24]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:
       [25]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-458
       8

     * [Yuan2018] Yaoshen Yuan, Leiming Yu, Zafer Doğan, 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:
       [26]https://www.spiedigitallibrary.org/journalArticle/Download?full
       DOI=10.1117%2F1.JBO.23.12.121618

1.5. 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, URL:
       [27]https://doi.org/10.1117/1.NPh.7.1.015009
     * Summary: PBM dosage over lifespan
     * Download: [28]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, URL: [29]https://doi.org/10.1117/1.NPh.7.1.015008
     * Summary: Brain2Mesh - a one-liner for brain mesh generator
       ([30]http://mcx.space/brain2mesh)
     * Download: [31]https://doi.org/10.1117/1.NPh.7.1.015008

     * [Cassano2019] Tran AP+, Cassano P+, 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: [32]https://doi.org/10.1117/1.NPh.6.1.015004

     * [Draghici2018] Draghici AE, Potart D, Hollmann JL, Pera V, Fang Q,
       DiMarzio CA, Andrew Taylor J, Niedre MJ, Shefelbine SJ, (2018)
       “Near infrared spectroscopy for measuring changes in bone
       hemoglobin content after exercise in individuals with spinal cord
       injury,” J Orthop Res. 36(1), 183-191, PMCID: PMC5711624
     * Summary: Use MCX to study NIR imaging of human bones in spinal cord
       injury
     * Download: [33]https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711624/

     * [Verleker2016] Verleker AP, Shaffer M, Fang Q, Choi, MR, Clare S.
       Stantz KM*, (2016) “Optical dosimetry probes to validate Monte
       Carlo and Empirical-method based NIR dose planning in the brain”,
       Appl. Optics, 55(34) 9875-9888, PMCID: PMC5483856
     * Summary: Optical dosimetry study using MCX for photodynamic therapy
       (PDT) in the brain
     * Download: [34]https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483856/

References

   1. http://mcx.space/wiki/index.cgi?action=rss
   2. https://mcx.space/wiki/index.cgi?Citation#MCX
   3. https://mcx.space/wiki/index.cgi?Citation#MCX_CL
   4. https://mcx.space/wiki/index.cgi?Citation#MMC
   5. https://mcx.space/wiki/index.cgi?Citation#General_MC_algorithm
   6. https://mcx.space/wiki/index.cgi?Citation#Applications
   7. https://doi.org/10.1117/1.JBO.27.8.083015
   8. https://doi.org/10.1117/1.JBO.27.8.083008
   9. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-11-11-6262
  10. http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178
  11. https://doi.org/10.1117/1.JBO.23.1.010504
  12. https://doi.org/10.1117/1.JBO.27.8.083014
  13. https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147
  14. http://dx.doi.org/10.1117/1.JBO.24.11.115002
  15. http://dx.doi.org/10.1117/1.JBO.24.2.020503
  16. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171
  17. https://doi.org/10.1117/1.JBO.17.10.106009
  18. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223
  19. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-2-5-1258
  20. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165
  21. https://doi.org/10.1088/1361-6560/acd48c
  22. https://doi.org/10.1117/1.jbo.27.8.083019
  23. https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202000377
  24. https://www.biorxiv.org/content/10.1101/2020.02.16.951590v2
  25. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-4588
  26. https://www.spiedigitallibrary.org/journalArticle/Download?fullDOI=10.1117/1.JBO.23.12.121618
  27. https://doi.org/10.1117/1.NPh.7.1.015009
  28. https://doi.org/10.1117/1.NPh.7.1.015009
  29. https://doi.org/10.1117/1.NPh.7.1.015008
  30. http://mcx.space/brain2mesh
  31. https://doi.org/10.1117/1.NPh.7.1.015008
  32. https://doi.org/10.1117/1.NPh.6.1.015004
  33. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711624/
  34. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483856/
