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| Monte Carlo eXtreme (MCX) is written by Qianqian Fang. | ||
| Qianqian is currently an Associate Professor in the | ||
| Department of Bioengineering at Northeastern University, USA. | ||
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| Address: Dept. of Bioengineering | ||
| Northeastern University | ||
| 360 Huntington Ave, ISEC 206, Boston, MA 02115, USA | ||
| URL: http://fanglab.org | ||
| Email: <q.fang at neu.edu> | ||
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| MCX Website : http://mcx.space | ||
| MCX Wiki: http://mcx.space/wiki | ||
| Source Code: http://github.com/fangq/mcx |
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| ############################################################ | ||
| # MCX Monte Carlo Photon Simulator Packaging System | ||
| # | ||
| # Author: Qianqian Fang <q.fang at neu.edu> | ||
| ############################################################ | ||
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| PKGNAME=mcx | ||
| VERSION=1.0.0 | ||
| SOURCE=src | ||
| GUI=mcxstudio | ||
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| all: bin/$(PKGNAME) bin/$(GUI) mex deb rpm | ||
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| bin/$(PKGNAME): | ||
| -$(MAKE) -C $(SOURCE) static | ||
| bin/$(GUI): | ||
| -$(MAKE) -C $(GUI) | ||
| -$(COPY) -a $(GUI)/debug/$(GUI) bin | ||
| mex: | ||
| -$(MAKE) -C $(SOURCE) mex | ||
| oct: | ||
| -$(MAKE) -C $(SOURCE) oct | ||
| deb: bin/$(PKGNAME) | ||
| -package/mcxpkg/mcxdebmkdir.sh $(PKGNAME) | ||
| -package/mcxpkg/mcxdebcopy.sh $(PKGNAME) $(VERSION) | ||
| -dpkg -b debian $(PKGNAME)-$(VERSION).deb | ||
| mexdeb: oct | ||
| -package/mcxpkg/mcxdebmkdir.sh $(PKGNAME)lab | ||
| -package/mcxpkg/mexdebcopy.sh $(PKGNAME)lab $(VERSION) | ||
| -dpkg -b debian $(PKGNAME)lab-$(VERSION).deb | ||
| guideb: bin/$(GUI) | ||
| -package/mcxpkg/mcxdebmkdir.sh $(PKGNAME)studio | ||
| -package/mcxpkg/guidebcopy.sh $(PKGNAME)studio $(VERSION) | ||
| -dpkg -b debian $(PKGNAME)studio-$(VERSION).deb | ||
| rpm: | ||
| -package/mcxpkg/mcxrpmmkdir.sh $(PKGNAME) | ||
| -package/mcxpkg/mcxrpmcopy.sh $(PKGNAME) $(VERSION) | ||
| cd rpmroot && tar zcvf $(PKGNAME)-$(VERSION).tar.gz $(PKGNAME) ; \ | ||
| rpmbuild --define="_topdir rpmroot/rpm" -ta $(PKGNAME)-$(VERSION).tar.gz | ||
| clean: | ||
| -$(MAKE) -C $(SOURCE) clean | ||
| -$(MAKE) -C $(GUI) clean | ||
| -rm -rf debian rpmroot pkg.info $(PKGNAME)*-$(VERSION).deb $(PKGNAME)*-$(VERSION)*.rpm | ||
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| .DEFAULT_GOAL := bin/$(PKGNAME) | ||
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| ============================================================= | ||
| Monte Carlo eXtreme (MCX) Suite | ||
| version 2021.2 | ||
| ============================================================= | ||
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| Copyright (c) 2010-2021 Qianqian Fang <q.fang at neu.edu> | ||
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| - 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: http://github.com/mcextreme/ | ||
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| ============================================================= | ||
| :: Acknowledgement: | ||
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| 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: | ||
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| 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. | ||
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| The full text of the software license can be found at | ||
| https://www.gnu.org/licenses/gpl-3.0.en.html | ||
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| To continue installation, you must agree with the above license. | ||
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| ============================================================= | ||
| :: Citation: | ||
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| The technical details of the software tools included in this | ||
| package can be found in the below publications. | ||
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| If you use MCX/MMC/MCX-CL in your research, you agree to | ||
| cite the relevant papers in your publications. | ||
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| === MCX === | ||
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| [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 | ||
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| [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 | ||
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| === MCX-CL === | ||
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| [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 | ||
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| === MMC === | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| === General MC algorithm === | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| [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 | ||
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| === Applications === | ||
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| [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 | ||
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| [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 | ||
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| [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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| ============================================================= |
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