COTI Lab Publications

1.1. Journal Articles

1.2. Computer-science conference papers

1.3. Conference papers

1.4. Thesis

1.5. Magazine article

1.6. Book chapters

1.1. Journal Articles

2020

• 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.
• Shijie Yan, Ruoyang Yao, Xavier Intes, and Qianqian Fang*, (2020) "Accelerating Monte Carlo modeling of structured-light-based diffuse optical imaging via 'photon sharing'," Opt. Lett. 45, 2842-2845
• 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: https://doi.org/10.1117/1.NPh.7.1.015009
• 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: https://doi.org/10.1117/1.NPh.7.1.015008

2019

• Qianqian Fang* and Shijie Yan, “Graphics processing unit-accelerated mesh-based Monte Carlo photon transport simulations,” J. of Biomedical Optics, 24(11), 115002 (2019).
• 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).
• 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

2018

• 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).
• Andreas Horn, Ningfei Li, Till A Dembek, Ari Kappel, Chadwick Boulay, Siobhan Ewert, Anna Tietze, Andreas Husch, Thushara Perera, Wolf-Julian Neumann, Marco Reisert, Hang Si, Robert Oostenveld, Christopher Rorden, Fang-Cheng Yeh, Qianqian Fang, Todd M Herrington, Johannes Vorwerk, Andrea A Kuehn, "Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging", Neuroimage. 2018 Sep 1;184:293-316 doi: https://doi.org/10.1101/322008
• Ruoyang Yao, Xavier Intes, and Qianqian Fang, "Direct approach to compute Jacobians for diffuse optical tomography using perturbation Monte Carlo-based photon “replay”," Biomed. Opt. Express 9, 4588-4603 (2018)
• Leiming Yu, Fanny Nina-Paravecino, David Kaeli, and Qianqian Fang*, "Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms," J. Biomed. Optics Letters, 23(1) 010504 2018.
• Bin Deng, Mats Lundqvist, Qianqian Fang, Stefan Carp, "Impact of errors in experimental parameters on reconstructed breast images using diffuse optical tomography," Biomed Optics Express, 9(3):1130-1150 2018

2017

• Adina E Draghici,Diane Potart,Joseph L Hollmann,Vivian Pera,Qianqian Fang,Charles A DiMarzio,J Andrew Taylor,Mark J Niedre,Sandra J Shefelbine, "Near infrared spectroscopy for measuring changes in bone hemoglobin content after exercise in individuals with spinal cord injury," J Orthop Res. May 2017 doi: 10.1002/jor.23622.
• Zimmermann B, Deng B, Singh B, Martino M, Selb J, Fang Q, Sajjadi AY, Cormier J, Moore RH, Kopans DB, Boas DA, Saksena MA, Carp SA. “Multimodal breast cancer imaging using coregistered dynamic diffuse optical tomography and digital breast tomosynthesis,” Journal of Biomedical Optics 22 (4), 046008-046008, 2017
• A. Horn, M. Reich, J. Vorwerk, N. Li, G. Wenzel, Q. Fang, T. Schmitz-Hübsch, R. Nickl, A. Kupsch, J. Volkmann, A.A. Kühn, M.D. Fox, “Connectivity predicts deep brain stimulation outcome in Parkinson's disease,” Ann. Neurol. (2017), 10.1002/ana.24974
• Sajjadi A, Isakoff SJ, Deng B, Singh B, Wanyo CM, Fang Q, Specht MC, Schapira L, Moy Beverly, Bardia A, Boas DA, Carp S, “Normalization of compression-induced hemodynamics in patients responding to neoadjuvant chemotherapy monitored by dynamic tomographic optical breast imaging (DTOBI)”, Biomed Optics Express, 8(2), pp. 555-569, 2017
• Verleker AP, Fang Q, Shaffer M, Clare S. Choi, MR, Stantz KM, “Optical dosimetry probes to validate Monte Carlo and Empirical-method based NIR dose planning in the brain”, Appl. Optics, 2016, Vol. 56, Issue 4, pp. 1131-1131 (2017).

2016

• Zimmermann B, Fang Q, Boas D, Carp S*, (2016) “Frequency domain near-infrared multiwavelength imager design using high-speed, direct analog-to-digital conversion,” J. Biomed. Opt. 21(1), 016010 (Jan 26, 2016)
• Yao R, Intes X, Fang Q* (2016), "Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation," Biomed. Optics Express, 7(1), 171-184

2015

• Deng B, Fradkin M, Rouet JM, Moore RH, Kopans DB, Boas DA, Lundqvist M, and Fang Q, "Characterizing breast lesions through robust multi-modal data fusion using independent diffuse optical and x-ray breast imaging," Journal of Biomed. Optics Letters, 20(8), 080502, 2015
• Deng B, Brooks DH, Boas DA, Lundqvist M, and Fang Q, "Characterization of structural-prior guided optical tomography using realistic breast models derived from dual-energy x-ray mammography," Biomed. Opt. Express 6(7), 2366-2379, 2015
• Gagnon L, Sakadžić S, Lesage F, Musacchia JJ, Lefebvre J, Fang Q, et al., “Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe,” J Neurosci.35(8):3663-75, 2015

before 2015

• Selb J, Ogden TM, Dubb J, Fang Q, and Boas DA, “Comparison of a layered slab and an atlas head model for Monte Carlo fitting of time-domain NIRS data of the adult head,” Journal of Biomedical Optics, 19(1), pp. 16010, 2014
• Carp SA, Sajjadi1 AY, Wanyo CM, Fang Q, Specht M, Schapira L, Moy B, Bardia A, Boas DA, Isakoff SJ, “Hemodynamic signature of breast cancer under fractional mammographic compression using a dynamic diffuse optical tomography system,” Biomed. Opt. Express, 4(12) 2911-2924, 2013
• Fang Q and Kaeli D, "Accelerating mesh-based Monte Carlo method on modern CPU architectures," Biomed. Opt. Express, 3(12), 3223-3230, 2012
• Chen J, Fang Q, Intes X, "Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography," Journal of Biomedical Optics, 17(10), 106009 2012
• Cooper RJ, Caffini M, Dubb J, Fang Q, Custo A, Tsuzuki D, Fischl B, Wells W 3rd, Dan I, Boas DA, "Validating atlas-guided DOT: A comparison of diffuse optical tomography informed by atlas and subject-specific anatomies," NeuroImage. 62(3), 1999-2006, 2012
• Perdue KL, Fang Q, Diamond, SG, “Quantitative assessment of diffuse optical tomography sensitivity to the cerebral cortex using a whole-head probe”, Phys. Med. Biol. 57, 2857-2872, 2012.
• Baraghis E, Devor A, Fang Q, Srinivasan VJ, Wu W, Boas D and Sakadžić S, "Two-photon microscopy of cortical NADH fluorescence intensity changes: correcting contamination from the hemodynamic response," J Biomed Opt 16, 106003 2011.
• Fang Q, “Comment on ‘A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation’,” Biomed. Opt. Express, vol. 2, issue 5, pp. 1258-1264, 2011.
• Fang Q, Selb J, Carp SA, Kopans DB, Moore RH, Brooks DH, Miller EL, Boas DA, “Combined optical and tomosynthesis breast imaging,” Radiology, (cover article) vol. 258, No. 1, pp. 89-97, 2011.
• Fang Q, “Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates,” Biomedical Optics Express, vol. 1, issue 1, pp. 165-175, 2010.
• Fang Q, Moore RH, Kopans DB, Boas DA, “Compositional-prior-guided image reconstruction algorithm for multi-modality imaging,” Biomedical Optics Express, vol. 1, issue 1, pp. 223-235, 2010.
• Fang Q, Meaney PM, Paulsen KD, “Viable three-dimensional microwave imaging, theory and experiments,” IEEE Trans. on Antennas and Propagation, vol. 58, No. 2, pp. 449– 458, 2010.
• Fang Q and Boas D, “Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units,” Optics Express, featured article, vol. 17, issue 22, pp. 20178-20190, 2009.
• Zhu G, Popovic M, Fang Q, “Microwave-induced thermoacoustics: assisting microwave tomography,” IEEE Trans. on Magnetics, vol. 45, issue 3, pp. 1654-1657, 2009.
• Fang Q, Carp SA, Selb J, Boverman G, Zhang Q, Kopans DB, Moore RH, Brooks DH, Miller EL, Boas DA, “Combined optical Imaging and mammography of the healthy breast: optical contrast derives from breast structure and compression,” IEEE Trans. Medical Imaging, vol. 28, issue 1, pp. 30 – 42, Jan. 2009.
• Fang Q, Sakadžić S, Ruvinskaya L, Devor A, Dale AM, Boas DA,"Oxygen advection and diffusion in a three dimensional vascular anatomical network," Optical Express, featured article, vol. 16, Issue 22, pp. 17530-17541, 2008.
• Carp SA, Selb J, Fang Q. Moore R, Kopans DB, Rafferty E, Boas DA, “Dynamic functional and mechanical response of breast tissue to compression,” Optical Express, vol. 16, Issue 20, pp. 16064-16078, 2008.
• Boverman G, Miller EL,Brooks DH, Fang Q, Boas DA, "Estimation and Statistical Bounds for Three-Dimensional Polar Shapes in Diffuse Optical Tomography," IEEE Transactions on Medical Imaging, vol. 27, issue 6, pp.752 – 765, Jun 2008.
• Boverman G, Fang Q, Carp SA, Miller EL, Brooks DH, Selb J, Moore RH, Kopans DB, Boas DA, "Spatio-Temporal Imaging of the Hemoglobin in the Compressed Breast With Diffuse Optical Tomography," Phys. Med. Biol. 52 3619-3641, 2007.
• Meaney PM, Fanning MW, Raynolds T, Fox CJ, Fang Q, Kogel CA, Poplack SP, Paulsen KD, "Initial Clinical Experience with Microwave Breast Imaging in Women with Normal Mammography," Acad Radiol., vol. 14, pp. 207-218, 2007.
• Meaney PM, Fang Q, Rubaek T, Paulsen KD, “Log transformation benefits parameter estimation in microwave tomographic imaging,” Medical Physics, 34 (6):2014-23, Jun 2007
• Carp SA, Kauffman T, Fang Q, Rafferty E, Moore R, Kopans D, Boas D, “Compression-induced changes in the physiological state of the breast as observed through frequency domain photon migration measurements,” Journal of Biomedical Optics, vol. 11, issue 6, Nov./Dec. 2006.
• Fang Q, Meaney PM, Paulsen KD, “The multi-dimensional phase unwrapping integral and applications to microwave tomographical image reconstruction,” IEEE Transaction on Image Processing, vol 15, No. 11, pp. 3311-3324, Nov. 2006.
• Fang Q, Meaney PM, Paulsen KD, “Singular value analysis of the Jacobian matrix in microwave image reconstruction,” IEEE Transactions on Antenna and Propagation, vol. 54, No. 8, pp.2371-2380, Aug. 2006.
• Fang Q, Meaney PM, Paulsen KD, “Microwave image reconstruction of tissue property dispersion characteristics utilizing multiple frequency information”, IEEE Transactions on Microwave Theory and Techniques, vol. 52, No. 8, pp. 1866-1875, Aug. 2004.
• Fang Q, Meaney PM, Geimer SD, Streltsov AV, Paulsen KD, “Microwave image reconstruction from 3D fields coupled to 2D parameter estimation,” IEEE Transactions on Medical Imaging, vol. 23, pp. 475-484, Apr. 2004.
• Meaney PM, Fanning MW, Paulsen KD, Li D, Pendergrass SA, Fang Q, Moodie KL, “Microwave thermal imaging: Initial in vivo experience with a single heating zone”, International Journal of Hyperthermia, vol. 19, pp. 617-641, 2003.
• Meaney PM, Paulsen KD, Fanning MW, Li D, Fang Q, “Image accuracy improvements in microwave tomographic thermometry: phantom experience”, International Journal of Hyperthermia, vol. 19, pp. 534-550, 2003.

1.2. Computer-science conference papers

• Yu L, Gong X, Sun Y, Fang Q, Rubin N and Kaeli D, "Moka: Model-based Concurrent Kernel Analysis", IEEE International Symposium on Workload Characterization, 2017.
• Paravecino F, Yu L, Kaeli D, Fang Q*, “Portable performance for Monte Carlo simulations of photon migration in 3D turbid media for single and multiple GPUs”, GTC2016, Paper#S6635, 2016, CA

1.3. Conference papers

• Vanegas M, Sun X, Fang Q, "Towards a fiberless, modular, and wearable full-head fNIRS system with built-in 3D self-calibrating orientation sensor network," fNIRS Conference 2018, Tokyo, Japan
• Yuan Y, Yu L, and Fang Q*, “Denoising in Monte Carlo Photon Transport Simulation Using GPU-accelerated Adaptive Non-Local Mean Filter,” OSA BIOMED 2018, Paper#JTh3A.41, FL
• Yu L, Nina-Paravecino F, Kaeli D, Fang Q*, “Fast Monte Carlo Photon Transport Simulations for Heterogeneous Computing Systems,” OSA BIOMED 2018, Paper#2912790, FL
• Vanegas M, Zimmerman B, Sahin S, Carp S, Fang Q*, “A Mobile Phone Based Reflectance Pulse Oximeter,” OSA BIOMED 2018, Paper#JTu3A.64, FL
• Vanegas M, Carp S, Fang Q*, “Mobile Phone Camera Based Near-Infrared Spectroscopy Measurements,” OSA BIOMED 2018, Paper#JTu3A.64, FL
• Yan S, Tran AP, Fang Q*, “A Dual-Mesh Monte Carlo Algorithm Using a Coarse Tetrahedral Mesh and Voxel Output”, OSA BIOMED 2018, Paper# JTh3A.17, FL
• Tran AP, Fang Q*, “Generating High Quality Tetrahedral Meshes of the Human Head and Applications in fNIRS,” OSA BIOMED 2018, Paper#JTu3A.52, FL
• Ruoyang Y, Intes X, Fang Q*, “Efficient Jacobian Construction for Hyperspectral Wide-field Diffuse Optical Tomography via Replay Monte Carlo,” OSA BIOMED 2018, Paper#JTu3A.30, FL
• Xu E, Fang Q*, “Optical Tomography Reconstruction to Recover Small Oriented Inclusions from Optically-Thick Diffusive Media”, OSA BIOMED 2018, Paper#JTu3A.67, FL
• Sahin S†, Sun X†, Vanegas M, Tran AP, Fang Q*, “Developing an Anatomically Accurate Multi-layered Optical Brain Phantom for fNIRS Studies”, OSA BIOMED 2018, Paper#JW3A.70, FL
• Deng B, Fang Q, Boas DA, Carp S*, “Impact of Experimental Parameter Errors on Reconstructed Breast Images Using Diffuse Optical Tomography,” OSA BIOMED 2016, Paper#2455560, FL
• Inacio D, Deng B, Kopans D, Boas D, Fang Q*, (2016) “Automatically finding tumors using structural-prior guided optical tomography,” OSA BIOMED 2016, Paper#2468528, FL
• Yao R, Intes X, Fang Q*, "Enabling wide-field illumination and detection in mesh-based Monte Carlo simulations ," OSA BIOMED 2016, Paper#2459052, FL
• Deng B, Brooks, DH, Boas DA, Lundqvist M, Fang Q* “Characterization of Breast Lesions Using Structural Prior Guided Optical Tomography on the Realistic Breast Model – DigiBreast,” OSA BIOMED 2016, Paper#2458069, FL
• Fang Q, “Quantitative diffuse optical tomography using a mobile phone camera and automatic 3D photo stitching,” OSA Biomedical Optics (BIOMED) conference, Apr. 2012.
• Fang Q, Carp SA, Martino M, Moore RH, Kopans DB, and Boas DA, “Joint image reconstruction for breast tumor diagnosis using both structural and functional information,” OSA Biomedical Optics (BIOMED) conference, Apr. 2012.
• Fang Q and Boas D, “GPU accelerated Monte Carlo simulation for 3D photon migration”, OSA Biomedical Optics (BIOMED) conference, Apr. 2010.
• Fang Q, Carp SA, Moore RH, Kopans DB, Boas DA, “Imaging Benign and Malignant Breast Lesions with Combined Optical Imaging and Tomosynthesis,” OSA Biomedical Optics (BIOMED) conference (invited), Apr. 2010.
• Fang Q and Boas D, “Tetrahedral mesh generation from volumetric binary and gray-scale images”, IEEE International Symposium on Biomedical Imaging (ISBI’09), 1142-1145, 2009.
• Zhu G, Popovic M, Fang Q, “Microwave-Induced Thermoacoustics: Assisting Microwave Tomography,” 13th Biennial IEEE Conference on Electromagnetic Field Computation, OB2-1, Athens, May 2008
• Fang Q, Carp SA, Selb J, Moore RH, Kopans DB, Miller EL, Brooks DH, Boas DA, "A multi-modality image reconstruction platform for diffuse optical tomography," OSA Biomedical Optics (BIOMED) conference, 2008.
• Fang Q, Carp SA, Selb J, Moore RH, Kopans DB, Miller EL, Brooks DH, Boas DA, "Spectrally Constrained Optical Breast Imaging with Co-registered X-Ray Tomosynthesis," OSA Biomedical Optics (BIOMED) conference, 2008.
• Fang Q, Meaney PM, Paulsen KD, “Phase unwrapping in the presence of scattering nulls and applications to microwave imaging,” Proceeding (425) Antennas, Radar, and Wave Propagation, Jul. 2004

1.4. Thesis

• Qianqian Fang, "Computational methods for microwave medical imaging," Ph.D. dissertation, Dartmouth College, Hanover, NH, 2004, Thesis Committee: Profs. Paul M. Meaney, Keith D. Paulsen, William Lotko, Eric L. Miller

1.5. Magazine article

• Fang Q, "Multi-modality breast imaging combining structure and function in breast cancer diagnosis", Diagnostic Imaging Europe, Vol. 27 No. 7, 13-16, 2011.

1.6. Book chapters

• Nina-Paravecino F., Yu L, Fang Q, and Kaeli D, “High-performance Monte Carlo Simulations for Photon Migration and Applications in Optical Brain Functional Imaging”, Handbook on Smart Healthcare, Springer (in press)
• Carp S, Fang Q, “Diffuse optical medical imaging,” in “Pathobiology of Human Disease (PHD),” Elsevier, 2013
• Venugopal V, Fang Q and Intes X, “Chapter 2. Multimodal Diffuse Optical Imaging”, in "Biophotonics for medical applications", Woodhead Publishing, 2012
• Fang Q, Carp S, Selb J, Boas D, “Chapter 9. Optical Imaging and X-ray Imaging”, Translational multimodality Optical Imaging, Azar FS, Intes X (Eds.), Artech House, Norwood, 2008
• Meaney PM, Fang Q, “Chapter 7. Microwave imaging: A model-based approach”, Alternative Breast Imaging-Four Model-Based Approaches, Paulsen KD, Meaney PM, Gilman L(Eds.), Kluwer, 2004.