Publication

Journal manuscript​

• Cao S, Ko M, Li C, Brown D, Wang X, Hu F, Gan Y.  Single-Belt vs. Split-Belt: Intelligent Treadmill Control via Micro-Phase Gait Capture for Post-stroke Rehabilitation. IEEE Transaction on  Human-Machine Systems. 2023, Accepted.

• Li X, Dong Z, Liu H, Kang-Mieler JJ, Ling Y, Gan Y. Frequency-aware optical coherence tomography image super-resolution via conditional generative adversarial neural network. Biomedical Optics Express. 2023 Oct 1;14(10):5148-61.

• Miao B, Hu Z, Mezzadra R, Hoeijmakers L, Fauster A, Du S, Yang Z, Sator-Schmitt M, Engel H, Li X, Broderick C....Gan Y.....Sun C. CMTM6 shapes antitumor T cell response through modulating protein expression of CD58 and PD-L1. Cancer cell.:S1535-6108.

• Huang Z, Gan Y, Lye T, Liu Y, Zhang H, Laine A, Angelini E, Hendon C. Cardiac Adipose Tissue Segmentation via Image-Level Annotations. IEEE Journal of Biomedical and Health Informatics. 2023 Apr 6.

• Li X, Dong Z, Liu H, Kang-Mieler JJ, Ling Y, Gan Y. Frequency-aware optical coherence tomography image super-resolution via conditional generative adversarial neural network. Biomedical Optics Express. 2023 Oct 1;14(10):5148-61. 

• Liu H, Li X, Bamba AL, Song X, Brott BC, Litovsky SH, Gan Y. Toward reliable calcification detection: calibration of uncertainty in object detection from coronary optical coherence tomography images. Journal of Biomedical Optics. 2023 Mar;28(3):036008.

• Ling, Y., Dong, Z., Li, X., Gan, Y. and Su, Y., 2023. Deep learning empowered highly compressive SS-OCT via learnable spectral–spatial sub-sampling. Optics Letters, 48(7), pp.1910-1913.

• M. Wang, Y. Ling, Z. Dong, X. Yao, Y. Gan, C. Zhou, and Y. Su, “GPU-accelerated iterative method for FD-OCT image reconstruction with an image-level cross-domain regularizer,” Opt. Express, vol. 31, no. 2, pp. 1813–1831, 2023.

• J. Garvin, F. Abushakra, Z. Choffin, B. Shiver, Y. Gan, L. Kong, and N. Jeong, “Microwave imaging for watermelon maturity determination,” Current Research in Food Science, vol. 6, p. 100 412, 2023, issn: 2665-9271.

• Li X, Cao S, Liu H, Yao X, Brott BC, Litovsky SH, Song X, Ling Y, Y. Gan. Multi-scale reconstruction of undersampled spectral-spatial OCT data for coronary imaging using deep learning. IEEE Transactions on Biomedical Engineering. 2022 May 20.

• Li, J., Jin, P., Zhu, J., Zou, H., Xu, X., Tang, M., Zhou, M., Y. Gan, He, J., Ling, Y. and Su, Y., 2021. Multi-scale GCN-assisted two-stage network for joint segmentation of retinal layers and discs in peripapillary OCT images. Biomedical Optics Express, 12(4), pp.2204-2220. [code]

• H. Liu, S. Cao, Y. Ling, and Y. Gan, “Inpainting for saturation artifacts in optical coherence tomog-raphy using dictionary-based sparse representation,”IEEE Photonics Journal, vol. 13, no. 2, pp. 1–10 [code]

• Y. Ling, M. Wang, X. Yao, Y. Gan, L. Schmetterer, C. Zhou, and Y. Su, “On the spectral leakageand speckle formation in fourier-domain optical coherence tomography,” Optics Letter, 2020, [code]

• Y. Wu, M. Zhang, Y. Gan, and C. Zhao, “Augment reality based teaching practice,” Biomedical Engineering Education, 2020.

• S. Kim, Y. Gan, and J. Irizarry. "Framework for UAS-Integrated Airport Runway Design Code Compliance Using Incremental Mosaic Imagery." Journal of Computing in Civil Engineering 35.2 (2020): 04020070.

• X. Chen, A. Miller, S. Cao, Y. Gan, J. Zhang, Q. He, R. Wang, X. Yong, P. Qin, B. Lapizco-Encinas, K. Du. Rapid Escherichia coli (E. coli) Trapping and Retrieval from Bodily Fluids via a Three-Dimensional (3D) Beads Stacked Nano-Device. ACS Applied Materials & Interfaces. 2020 Jan 15 (Featured complementary cover).

• Y. Gan, T. H. Lye, C. C. Marboe, and C. P. Hendon, “Characterizationof the human myocardiumby optical coherence tomography,”Journal of biophotonics, e201900094, 2019

• D. Mojahed, R.S Ha, P. Chang, Y. Gan, X. Yao, B. Angelini, H. Hibshoosh, B. Taback, C. P. Hendon, “Fully Automated Postlumpectomy Breast Margin Assessment Utilizing Convolutional Neural Network Based Optical Coherence Tomography Image Classification Method”, Academic Radiology, 2019.

• L. Shi, W. Yao, Y. Gan, L. Zhao, W.E. McKee, J. Vink, R. Wapner, C. Hendon, K. Myers, “Anisotropic Material Characterization of Human Cervix Tissue based on Indentation.” Journal of biomechanical engineering, 2019, Jun 12.

• X. Ji, A. Klenner, X. Yao, Y. Gan, A. Gaeta, C. P. Hendon, M. Lipson, “Chip-based frequency comb source for optical coherence tomography” Optics Express 27(14), 19896-19905

• C.P. Hendon, T.H. Lye, X. Yao, Y. Gan, C.C. Marboe, "Optical coherence tomography imaging of cardiac substrates" Quantitative Imaging in Medicine and Surgery, 2019, 9 (5), 882-904

• J.P. McLean, Y. Gan, T.H. Lye, D. Qu, H.H.. Lu, C.P. Hendon, "High-speed collagen fiber modeling and orientation quantification for optical coherence tomography imaging" Optics Express, 2019, 27 (10), 14457-14471

• X. Yao, Y. Gan, Y. Ling, and C. P. Hendon, “Multi-contrast endomyocardial imaging by single-channel high resolution cross-polarization optical coherence tomography,” Journal of Biophotonics, 2018, issn: 1864-0648.

• Y. Ling, Y. Gan, X. Yao, and C. Hendon, “Phase noise analysis on swept-source optical coherence tomography” Optics Letters, 2017, 42(7), 1333-1336.

• Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” Journal of Biomedical Optics, vol. 21, no. 10, p. 101 407, 2016.

• W. Yao*, Y. Gan*, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLOS ONE, vol. 11, no. 11, pp. 1–20, Nov. 2016, (*Equally contributed first author).

• X. Yao*, Y. Gan*, E. Chang, S. A. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Visualization and tissue classification of human breast cancer images using ultrahigh-resolution OCT,” Laser in surgery and medicine, 2016. (*Equally contributed first author, Selected as Feature of the Week on octnews.org).

• X. Yao, Y. Gan, C. C. Marboe, and C. P. Hendon, “Myocardial imaging using ultrahigh-resolution spectral domain optical coherence tomography,” Journal of Biomedical Optics, vol. 21, no. 6, p. 061 006, 2016.

• K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” Journal of Biomechanics, vol. 48, no.9, pp. 1533 –1540, 2015, Reproductive Biomechanics.

• Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomedical Optics Express, vol. 6, no. 4, pp. 1090–1108, Oct. 2015. [code]

• Y. Gan and C. P. Fleming, “Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography,” Biomedical Optics Express, vol. 4, no. 10, pp. 2150–2165, Oct. 2013.

• Y. Gan, et al. Multiple Rayleigh fading channels modeling based on sum‐of‐sinusoids model. International Journal of Communication Systems. 2014 Nov;27(11):2997-3012.

• Y. Gan et al, “An improved SoS method for generating multiple uncorrelated Rayleigh fading waveforms,” Communications Letters, IEEE, vol. 14, no. 7, pp. 641–643, 2010.

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Conference proceedings​

• X. Li, Y. Gan, D. Duan, and X. Yang, “Detecting and measuring human gastric peristalsis using magnetically controlled capsule endoscope,” in 2023 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2023.

• X. Li, H. Liu, X. Song, B. Brott, S. Litovsky, and Y. Gan, “Structural constrained virtual histology staining for human coronary imaging using deep learning,” in 2023 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2023.

• X. Li, S. Holiday, M. Cribbet, A. Bharadwaj, S. White, E. Sazonov, and Y. Gan, “Non-invasive screen exposure time assessment using wearable sensor and object detection,” in 2022 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2022, pp. 4917–4920.

• Z. Huang, H. Zhang, A. Laine, E. Angelini, C. P. Hendon, and Y. Gan, “Co-seg: An image segmenta-tion framework against label corruption,” in2021 IEEE 18th International Symposium on BiomedicalImaging (ISBI), 2021. [data & code]

• S. Gregory, H. Cheng, S. Newman, and Y. Gan, “Hydranet: A multi-branch convolutional neuralnetwork architecture for MRI denoising,” inSPIE Medical Imaging, 2021. [data & code]

• Z. Huang, Y. Gan, T. Lye, H. Zhang, A. F. Laine, E. Angelini, C. Hendon, "Heterogeneity Measurement of Cardiac Tissues Leveraging Uncertainty Information from Image Segmentation." In International Conference on Medical Image Computing & Computer Assisted Intervention (MICCAI 2020), 2020, Accepted.

• S. Cao, X. Yao, N. Koirala, B. Brott, S. Litovsky, Y. Ling, Y. Gan, "Super-resolution technology to simultaneously improve optical & digital resolution of optical coherence tomography via deep learning". in 2020 42th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Accepted

• Z. Huang, Y. Gan, T. Lye, D. Theagene, S. Chintapalli, S. Virdi, A. F. Laine, E. Angelini, C. Hendon, "Segmentation and Uncertainty Measures of Cardiac Tissues on Optical Coherence Tomography Via Convolutional Neural Networks." In IEEE 17th International Symposium on Biomedical Imaging (ISBI 2020), 2020.

• Y. Gan, J. Yang, B. M. Smith, P. Balte, E. Hoffman, C. P. Hendon, R. G. Barr, A. F. Laine, E. Angelini, "Enhanced Generative Model for Unsupervised Discovery of Spatially-Informed Macroscopic Emyphysema: The MESA COPD Study." In IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 1212-1215, 2019.

• D. Mojahed, P. Chang, Y. Gan, X. Yao, B. Angelini, H. Hibshoosh, R. Ha, C. P. Hendon "Convolution neural network classification of breast cancer in optical coherence tomography (OCT)" in Proc. SPIE, 2019, 10867-58.

• Ji X, Klenner A, Yao X, Y. Gan, Gaeta AL, Hendon CP, Lipson M. Chip-Based Frequency Combs for High-Resolution Optical Coherence Tomography. In CLEO: Science and Innovations 2018 May 13 (pp. STh1J-4). Optical Society of America.

• Y. Gan, Lye T, Yao X, Marboe C, Hendon C. Characterization of Human Endomyocardium Using a Human Cardiac Optical Coherence Tomography Atlas. InOptical Tomography and Spectroscopy 2018 Apr 3 (pp. OTh2D-6). Optical Society of America.

• T. Lye, Y. Gan, and C. P. Hendon, “Mapping the human atria with optical coherence tomography,” in Proc. SPIE, 2017, 10042-2.

• Y. Gan, X. Yao, D. Tsay, C. Marboe, and C. P. Hendon, “Characterization of ventricular endomyocardial tissue using optical coherence tomography,” in Proc. SPIE, 2017, 10042-6.

• W. Meiniel, Y. Gan, C. P. Hendon, J. C. Olivo-Mariri, A. Laine, and E. D. Angelini, “Sparsity-based simplification of spectral-domain optical coherence tomography images of cardiac samples,” in 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), Apr. 2016, pp. 373–376.

• Y. Gan, S. Gutbrod, I. R. Efimov, and C. P. Hendon, “Towards geometric modeling of the atria using optical coherence tomography,” in Biomedical Optics 2016, Optical Society of America, 2016, JM3A.26.

• Y. Gan, X. Yao, E. Chang, S. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Comparative study of texture features in OCT images at different scales for human breast tissue classification,” in 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Aug. 2016, pp. 3926–3929.

• Y. Gan, E. Angelini, A. Laine, and C. P. Hendon, “BM3D-based ultrasound image denoising via brushlet thresholding,” in Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, Apr. 2015, pp. 667–670.

• Y. Gan, W. Yao, K. Myers, and C. P. Hendon, “An automated 3D registration method for optical coherence tomography volumes,” in Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE, 2014, pp. 3873–3876.

Patents

• ​X. Ji, A. Klenner, X. Yao, Y. Gan, A. Gaeta, C. P. Hendon, and M. Lipson, “Chip-based frequency combs for high-resolution optical coherence tomography,” pat., 62/540,412 filed 08/02/2017

Conference presentation

• Y. Gan, J. Yang, B. M. Smith, P. Balte, E. Hoffman, C. P. Hendon, R. G. Barr, A. F. Laine, E. Angelini, "Enhanced Generative Model for Unsupervised Discovery of Spatially-Informed Macroscopic Emyphysema: The MESA COPD Study." in 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI). Accepted.

• D. Mojahed, P. Chang, Y. Gan, X. Yao, B. Angelini, H. Hibshoosh, R. Ha, C. P. Hendon "Convolution neural network classification of breast cancer in optical coherence tomography (OCT)" SPIE Photonics West BiOS, San Francisco, CA, Feb. 2019, Oral Presentation.

• T. Lye,  Y. Gan, K. P. Vicent, A. McCulloch, and C. P. Hendon, "Comprehensive mapping and modeling of the human left atrium with optical coherence tomography" SPIE Photonics West BiOS, San Francisco, CA, Feb. 2019, Oral Presentation.

• Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Heterogeneity study of the human cervix between the internal os and the external os using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2018, Oral Presentation.

• X. Yao,  Y. Gan, Y. Ling, C. Marboe, and C. P. Hendon, “Functional endomyocardial imaging by single-channel high resolution cross-polarization oct,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2018, Oral Presentation.

• T. Lye,  Y. Gan, and C. P. Hendon, “Mapping the human atria with optical coherence tomography," in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• Y. Gan, T. H. Lye, X. Yao, and C. P. Hendon, “Visualization and deep learning from human cardiac OCT atlas,” in Biomedical Engineering Society (BMES) Annual Meeting, Phoenix, AZ, Oct. 2017.

• T. Lye, Y. Gan, and C. P. Hendon, “Mapping the human atria with optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Depth analysis of collagen directionality on axial human uterine cervical tissue using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• Y. Gan, X. Yao, D. Tsay, C. Marboe, and C. P. Hendon, “Characterization of ventricular endomyocardial tissue using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• Y. Gan, X. Yao, E. Chang, S. A. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Automated adipose map generation for assessing cancerous human breast tissue using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• X. Yao, Y. Gan, E. Chang, S. A. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Visualization and tissue classification of human breast cancer images using ultrahigh-resolution OCT,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2017, Oral Presentation.

• W. Meiniel, Y. Gan, C. P. Hendon, J.-C. Olivo-Marin, and E. Laine A.F.and Angelini, “Sparsity-based simplification of spectral-domain optical coherence tomography images of cardiac samples,” in Biomedical Imaging (ISBI), 2016 IEEE 12th International Symposium on, Prague, CZ, Apr. 2016, Poster Presentation.

• Y. Gan, S. Gutbrod, I. Efimov, and C. P. Hendon, “Towards geometric modeling of the atria using optical coherence tomography,” in Biomedical Optics, OSA, Fort Lauderdale, FL, Apr. 2016, Poster Presentation.

• Y. Gan, D Tsay, S. Amir, C. Marboe, and C. P. Hendon, “Automated tissue classification of intracardiac optical coherence tomography images,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2016, Oral Presentation.

• Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Dispersion analysis of collagen fiber networks in cervical tissue using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2016, Oral Presentation.

• Y. Gan, X. Yao, E. Chang, S. A. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Comparative study of texture features in OCT images at different scales for human breast tissue classification,” in Engineering in Medicine and Biology Society (EMBC), 2016 38th Annual International Conference of the IEEE, Orlando, FL, Aug. 2016, Poster Presentation.

• Y. Gan, X. Yao, E. Chang, S. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Texture features analysis in OCT images for human breast tissue classification,” in Laser in medicine and biology, 2016 Gordon Research Conference, Dover, VT, Jul. 2016, Poster Presentation.

• Y. Gan, X. Yao, D. Tsay, C. Marboe, and C. P. Hendon, “Automated cardiac tissue characterization using OCT,” in New England Sympoisum on Biomedical Optics, Cambridge, MA, Oct. 2016, Oral Presentation.

• X. Yao, Y. Gan, E. Chang, S. A. B. Amir, H. Hibshoosh, S. Feldman, and C. Hendon, “Ultrahigh-resolution OCT imaging of breast tissue with feature differentiation,” in Laser in medicine and biology, 2016 Gordon Research Conference, Dover, VT, Jul. 2016, Poster Presentation.

• S. B. Amir, Y. Gan, H. Hibshoosh, S. Feldman, and C. P. Hendon, “Towards characterization of ductal carcinoma in situ using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2015, Poster Presentation.

• S. Amir, Y. Gan, H. Hibshoosh, S. Feldman, and C. P. Hendon, “Towards characterization of breast tissue morphology using optical coherence tomography,” in International Symposium on Biomedical Imaging (ISBI), 2015 12th Annual International Coneference of the IEEE, Brooklyn, NY, Apr. 2015, Poster Presentation.

• Y. Gan, E. Angelini, A. Laine, and C. P. Hendon, “BM3D-based ultrasound image denoising via brushlet thresholding,” in International Symposium on Biomedical Imaging (ISBI), 2015 12th Annual International Conference of the IEEE, Brooklyn, NY, Apr. 2015, Poster Presentation.

• Y. Gan, D Tsay, S. Amir, C. Marboe, and C. P. Hendon, “Automated myocardial characterization using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2015, Oral Presentation.

• Y. Gan, D Tsay, S. Amir, C. Marboe, and C. P. Hendon, “Towards the automatic classification of endomyocardial tissues for intracardiac OCT,” in SPIE/NIH Biophotonics from Bench to Bedside, Bethesda, Maryland, Sep. 2015, Poster Presentation.

• Y. Gan, D. Tsay, C. Fung, C. C. Marboe, and C. P. Hendon, “Automated three dimensional segmentation of atrial optical coherence tomography images,” in Biomedical Engineering Society (BMES) Annual Meeting, Tampa, Florida, Oct. 2015, Poster Presentation.

• Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J.Wapner, and C. P. Hendon, “Three-dimensional ultrastructure study of cervical collagen fibers using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2015, Oral Presentation.

• W. Yao, Y. Gan, C. P. Hendon, J. Vink, R. Wapner, and K. M. Myers, “The collagen directionality and dispersion and mechanical indentaion response in nonpregnant human cervical tissue,” in Summer Biomachincs, Bioengineering and Biotransport Conference (SB3C), Snowbird, UT, Jun. 2015, Oral Presentation.

• K. M. Myers, J. Y. Vink, W. Yao, C. P. Hendon, and Y. Gan, “The constitutive modeling of human cervical tissue. world congress of biomechanics,” in World Congress of Biomechanics, Boston, MA, Jul. 2014, Oral Presentation.

• Y. Gan and C. P. Hendon, “Three-dimensional quantification of myofiber orientation and tractography using optical coherence tomography,” in SPIE Photonics West BiOS, San Francisco, CA, Feb. 2014, Oral Presentation.

• Y. Gan, W. Yao, K. Myers, and C. P. Hendon, “An automated 3D registration method for optical coherencetomography volumes,” in Engineering in Medicine and Biology Society (EMBC), 36th Annual International Conference of the IEEE, Chicago, IL, Aug. 2014, Oral Presentation.

• D. Tsay, Y. Gan, C. C. Marboe, and C. P. Hendon, “Feasibility of endomyocardial imaging using optical coherence tomography for the diagnosis of myocardial disease,” in Transcatheter cardiovascular therapeutics (TCT), Washington, DC, Sep. 2014, Poster Presentation.

• Y. Gan and C. P. Hendon, “Quantification of 3D fiber orientation for myocardial tissues using optical coherence tomography,” in Biomedical Engineering Society (BMES) Annual Meeting, Seattle, WA, Sep. 2013, Oral Presentation.