Papers

1.1. MCX
1.2. MCX-CL
1.3. MMC
1.4. General MC algorithm
1.5. 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

  • [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

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: https://doi.org/10.1117/1.JBO.23.1.010504

1.3. MMC

  • [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: 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

  • [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: https://doi.org/10.1117/1.JBO.17.10.106009

1.4. 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 simulations of multiple patterns
  • 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

1.5. Applications

  • [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: 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: 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: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483856/
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