Journal and Peer-reviewed Full Conference Publications:

2023
  1. Z. Yang and S. Farsiu, -- "Directional Connectivity-based Segmentation of Medical Images", CVPR, pp. 11525-11535, 2023-- Code
  2. R. Rasti, A. Biglari, M. Rezapourian, Z. Yang, and S. Farsiu, "RetiFluidNet: A Self-Adaptive and Multi-Attention Deep Convolutional Network for Retinal OCT Fluid Segmentation", IEEE Transactions on Medical Imaging , 42(5), pp. 1413 – 1423, May 2023 Open Source Software
  3. Z. Z. Zemborain, M. Soifer, N. S. Azar, S. Murillo, H. M. Mousa, V.L. Perez, S. Farsiu, " Open-Source Automated Segmentation of Neuronal Structures in Corneal Confocal Microscopy Images of the Subbasal Nerve Plexus with Accuracy on Par with Human Grading", Cornea , 42(10),pp. 1309-1319, Oct. 2023 Open Source Software, Dataset
  4. J. Loo, K.Y. C. Teo, C.H. Vyas, J.M. N. Jordan-Yu, A.B. Juhari, G.J. Jaffe, C. M. G. Cheung, and S. Farsiu " Joint multimodal deep learning-based automatic segmentation of ICGA and OCT images for assessment of PCV biomarkers", Opthalmology Science , 3(3),100292, Sept. 2023
  5. S. Soltanian-Zadeh, Z. Liu, Y. Liu, A. Lassoued, C.A. Cukrask, D.T. Miller, D.X. Hammer, and S. Farsiu, " Deep learning-enabled volumetric cone photoreceptor segmentation in adaptive optics optical coherence tomography images of normal and diseased eyes", Biomedical Optics Express , 14(2), pp.815-833, 2023 Annotated Dataset
  6. P.M, Hicks, K. Singh, N.V. Prajna, M. Lu, L.M. Niziol, M.F. Greenwald, A. Verkade, G. Amescua, S. Farsiu, M.A. Woodward, " Quantifying clinicians’ diagnostic uncertainty when making initial treatment decisions for microbial keratitis", Cornea, 42(11):p 1408-1413, November, 2023
  7. M.C. Lu, C. Deng, M.F. Greenwald, S. Farsiu, N. V. Pranja, N. Nallasamy, M. Parwar, J. N. Hart, S. Kochar, S. Selvaraj, H. Levine, G. Amescua, P. A.Sepulvedu-Beltran, L. M . Niziol, M.A. Woodward, " Automatic Classification of Slit-Lamp Photographs by Imaging Illumination", Cornea, (In Press), 2023
  8. Y. Sazhnyev, T.N. Sin, A. Ma, E. Chang, L. Huynh, K. Roszak, S. Park, K. Choy, S. Farsiu, A. Moshiri, S. M. Thomasy, G. Yiu, " Choroidal Changes in Rhesus Macaques in Aging and Age-Related Drusen", IOVS, 64(12):44, 2023

    9. 2022

  9. Z. Yang, S. Soltanian-Zadeh, and S. Farsiu, "BiconNet: An Edge-preserved Connectivity-based Approach for Salient Object Detection", Pattern Recognition, 121, 108231, Jan. 2022 Open Source Software
  10. K.C. Choy, G. Li, W. D. Stamer, S. Farsiu, "Open-Source Deep Learning-Based Automatic Segmentation of Mouse Schlemm’s Canal in Optical Coherence Tomography Images", Experimental Eye Research,214, 108844, 2022 Open Source Software and dataset
  11. K. C. Zhou, R. P. McNabb, R. Qian, S. Degan, A.H. Dhalla, S. Farsiu, and J.A. Izatt, "Computational 3D microscopy with optical coherence refraction tomography", Optica,9(6), pp. 593-601, 2022 Open Source Software and dataset News
  12. E. M. Lad, J. L. Duncan, W. Liang, M. G. Maguire, A. R. Ayala, I. Audo, D. G. Birch, J. Carroll, J. K. Cheetham, T. A. Durham, A. Fahim, J. Loo, Z. Deng, D. Mukherjee, E. Heon, R. B. Hufnagel, A. Iannaccone, G. J. Jaffe, C. N. Kay, M. Michaelides, M. E. Pennesi, A. Vincent, C. Y. Weng, and S. Farsiu, "Baseline Microperimetry and Optical Coherence Tomography in the RUSH2A Study: Structure-Function Association and Correlation with Disease Severity", American Journal of Ophthalmology, 244 , pp. 98-116, Dec. 2022
  13. J.R. Abraham, G.J. Jaffe, P.K. Kaiser, S.J. Chiu, J. Loo, S. Farsiu, L. Bouckaert, V. Karageozian, M. Sarayba, S.K. Srivastava, J.P. Ehlers, " Impact of Baseline Quantitative OCT Features on Response to Risuteganib for the Treatment of Dry Age-Related Macular Degeneration: The Importance of Outer Retinal Integrity", Ophthalmology Retina, 6(11), pp.1019-1027, NOV. 2022
  14. A. Hasan, J.M. Pereira, S. Farsiu, V. Tarokh, " Identifying Latent Stochastic Differential Equations", IEEE Transactions on Signal Processing, 70, 89-104,2022
  15. J. Loo, C.X. Cai, J. Choong, E. Chew, M. Friedlander, G.J. Jaffe, and S. Farsiu, " Deep learning-based classification and segmentation of retinal cavitations on optical coherence tomography images of macular telangiectasia type 2", British Journal of Ophthalmology, 106(3), pp. 396-402, March 2022
  16. J. Loo, G.J. Jaffe, J.L. Duncan, D.G. Birch, and S. Farsiu, " Validation of a deep learning-based algorithm for segmentation of the ellipsoid zone on optical coherence tomography images of an USH2A-related retinal degeneration clinical trial", Retina, 42(7), pp. 1347-1355, July 2022
  17. A. Hasan, K. Elkhalil, Y. Ng, J. M. Pereira, S. Farsiu, J. H. Blanchet, V. Tarokh, " Modeling Extremes with d-max-decreasing Neural Networks", 38th Conference on Uncertainty in Artificial Intelligence (UAI 2022), 2022

    18. 2021

  18. S. Soltanian-Zadeh, K. Kurokawa, Z. Liu, F. Zhang, O. Saeedi, D.X. Hammer, D.T. Miller, and S. Farsiu, "Weakly-supervised Individual Ganglion Cell Segmentation from Adaptive Optics OCT Images for Glaucomatous Damage Assessment", Optica, 8(5), pp. 642-651, May 2021 Annotated Data Set News
  19. Z. Yang, S. Soltanian-Zadeh, K. K. Chu, H. Zhang, L. Moussa, A.E. Watts, N.J. Shaheen, A. Wax, and S. Farsiu, "Connectivity-based Deep Learning Approach for Segmentation of the Epithelium in In Vivo Human Esophageal OCT Images", Biomedical Optics Express, 12(10), pp. 6326-6340, OCT. 2021 Annotated Dataset
  20. K.C. Zhou, C. Cooke, J. Park, R. Qian, R. Horstmeyer, J.A. Izatt, and S. Farsiu, "Mesoscopic photogrammetry with an unstabilized phone camera", CVPR, 7535-7545, 2021 Open Source Software and Data
  21. J. Loo, M.A. Woodward, N.V. Prajna, M.F. Kriegel, M. Pawar , M. Khan , L. Niziol, S. Farsiu, “Open-Source Automatic Biomarker Measurement on Slit-Lamp Photography to Estimate Visual Acuity in Microbial Keratitis”, Translational Vision Science & Technology, 10(2), October 2021 Open Source Software and Data
  22. J. Loo, M.F. Kriegel, M.M. Tuohy, K.H. Kim, V. Prajna, M.A. Woodward, and S. Farsiu, “Open-source automatic segmentation of ocular structures and biomarkers of microbial keratitis on slit-lamp photography images using deep learning”, IEEE Journal of Biomedical Health and Informatics, 5 (1), 88-99, Jan. 2021 Open Source Software and Data
  23. Z. Song, L. Xu, J. Wang, R. Rasti, A. Sastry, J.D. Li, W. Raynor, J.A. Izatt, C.A. Toth, L. Vajzovic, B. Deng, S. Farsiu, " Lightweight Learning-based Automatic Segmentation of Subretinal Blebs on Microscope-Integrated Optical Coherence Tomography Images", American Journal of Ophthalmology, , 221, 154-168, Jan. 2021
  24. K. Zhou, R. Qian, A.H. Dhalla, S. Farsiu, J.A. Izatt, " Unified k-space theory of optical coherence tomography", Advances in Optics and Photonics, 13(2),462-514, 2021 Open Access PrePrint
  25. K.C. Zhou, A.H. Dhalla, R. McNabb, R. Qian, S. Farsiu, J.A. Izatt, "High-speed multi-view imaging approaching 4pi steradians using conic section mirrors: theoretical and practical considerations", Journal of the Optical Society of America A, 38(12), pp.1810-1822, 2021
  26. C.X. Cai, J. Choong, S. Farsiu, S.J. Chiu, E.Y. Chew, and G.J. Jaffe, “Retinal Cavitations in Macular Telangiectasia Type 2 (MacTel): Longitudinal Structure-Function Correlations", British Journal of Ophthalmology, 105 (1), 109-112, Jan. 2021
  27. Y. Bao, S. Soltanian-Zadeh, S. Farsiu, Y. Gong, " Segmentation of Neurons from Fluorescence Calcium Recordings Beyond Real-time", Nature Machine Intelligence, 3, pp. 590–600 (2021)
  28. G. Li, C. Lee, A.T. Read, K. Wang, J. Ha, M. Kuhn, I. Navarro, J. Cui, K.M. Young, R. Gorijavolu, T. Sulchek, C.C. Kopczynski, S. Farsiu, J.R. Samples, P. Challa, C.R. Ethier, and W.D. Stamer. " Antifibrotic activity of a rho-kinase inhibitor restores outflow function and intraocular pressure homeostasis", eLife 10:e60831 2021.
  29. D.Y. Kim, J. Loo, S. Farsiu, G.J. Jaffe, " Comparison of Single Drusen Size on Color Fundus Photography and Spectral-Domain Optical Coherence Tomography", Retina, 41(8), pp1715-1722, Aug. 2021
  30. M.V. Pasricha, V. Tai, A. El-Hage-Sleiman, K. Winter, S.J. Chiu, S. Farsiu, S. S. Stinnett, E. M. Lad, W.T. Wong, E.Y. Chew, C.A. Toth, " Local anatomic precursors to new onset geographic atrophy in age-related macular degeneration as defined on optical coherence tomography", Ophthalmology Retina, 5(5), pp.396-408, May 2021.
  31. L. K. Mukkamala, J. Avaylon, R.J. Welsh, A. Yazdanyar, P. Emami-Naeini, S. Wong, J. Storkersen, J. Loo, D. Cunefare, S. Farsiu, A. Moshiri, S.S. Park, G. Yiu, " Intraoperative Retinal Changes May Predict Anatomic Outcomes after Epiretinal Membrane Peeling Surgery", Translational Vision Science & Technology, 10(2):36, Feb. 2021
  32. A. Sastry, J.D. Li, W. Raynor, C. Viehland, Z. Song, L. Xu, S. Farsiu, J.A. Izatt, C.A. Toth, L. Vajzovic, " Microscope-Integrated OCT-Guided Volumetric Measurements of Subretinal Blebs Created by a Suprachoroidal Approach", Translational Vision Science & Technology, 10(7):24, 2021
  33. K. Elkhalil, A. Hasan, J. Ding, S. Farsiu, V. Tarokh, " Fisher Auto-Encoders," The 24th International Conference on Artificial Intelligence and Statistics (AISTATS), PMLR 352-360,2021

    34. 2020

  34. K. Hagan, T. DuBose, D. Cunefare, G. Waterman, J. Park, C. Simmerer, A.N. Kuo, R.P. McNabb, J.A. Izatt, and S. Farsiu, " Multimodal handheld adaptive optics scanning laser ophthalmoscope", Optics Letters, 45(17), pp. 4940-4943, September 2020
  35. J. Loo, T.E. Clemons, E.Y. Chew, M. Friedlander, G.J. Jaffe, and S. Farsiu, " Beyond Performance Metrics: Automatic Deep Learning Retinal OCT Analysis Reproduces Clinical Trial Outcome", Ophthalmology, 127(6), pp. 793-801, June 2020
  36. R.Rasti, M.J. Allingham, P.S. Mettu, S. Kavusi, K. Govind, S.W. Cousins, and S. Farsiu, " "Deep Learning-based Single-shot Prediction of Differential Effects of Anti-VEGF Treatment in Patients with Diabetic Macular Edema"", Biomedical Optics Express, 11(2), pp. 1139-1152, Feb. 2020 News
  37. T.M. Tran; S. Kim, K.H. Lin, S.H. Chung, S. Park, Y. Sazhnyev, Y. Wang, D. Cunefare, S. Farsiu, S.M. Thomasy, A. Moshiri, G. Yiu, " "Quantitative Fundus Autofluorescence in Rhesus Macaques in Aging and Age-Related Drusen"", IOVS,61(16), , July 2020
  38. M.F. Kriegel, J. Loo, S. Farsiu, V. Prajna, M. Tuohy, K.H. Kim, A.N. Valicevic, L.M. Niziol, H. Tan, H.A. Ashfaq, D. Ballouz, M.A. Woodward, " Measurement Reliability for Anterior Segment and Keratitis Morphology", Cornea, 39(12):1503-1509, 2020
  39. O. Huang, W. Long, N. Bottenus, M. Lerendegui, G.E. Trahey, S. Farsiu, and M.L. Palmeri, " "MimickNet, Matching Clinical Post-Processing Under Realistic Black-Box Constraints"", IEEE Transactions on Medical Imaging,39(6), pp. 2277-2286, June 2020
  40. J.L. Duncan, W. Liang, M.G. Maguire, I. Audo, .R. Ayala, D.G. Birch, J. Carroll, J.K. Cheetham, S.D. Esposti, T.A. Durham, L. Erker, S. Farsiu, F.L. Ferris, E. Heon, R.B. Hufnagel, A. Iannaccone, G.J. Jaffe, C.N. Kay, M. Michaelides, M.E. Pennesi, J.A. Sahel, “Baseline Visual Field Findings in the RUSH2A Study: Associated Factors and Correlation with Other Measures of Disease Severity”, American Journal of Ophthalmology,, 219, pp. 87-100, Nov. 2020
  41. T.Y.A. Liu, S. Farsiu, D.S.W. Ting " Generative Adversarial Networks (GANs) to Predict Treatment Response for Neovascular Age-related Macular Degeneration: Interesting, but is it useful?", British Journal of Ophthalmology, 104(12), pp.1629-1630, 2020
  42. G. Li, H. Schmitt, W. Johnson, C. Lee, I. Navarro, J. Cui, T. Fleming, M. Gomez-Caraballo, M.H. Elliott, J M. Sherwood, M.A. Hauser, S. Farsiu, C.R. Ethier, and W.D. Stamer, “Integral role for lysyl oxidase-like-1 in conventional outflow tissue function and behavior”, ), The FASEB Journal,, 34(8), pp.10762-10777, August 2020
  43. G. Yiu, J. Roberts, I. Mollhoff, D. Cunefare, S. Chung, B. Shibata, Y. Wang, and S. Farsiu, U. Nguyen, S. Thomasy, “Long-term Evolution and Remodeling of Soft Drusen in the Nonhuman Primate”, Investigative Ophthalmology & Visual Science,61(2):32 2020
  44. K. Zhou, R. Qian, S. Farsiu, J.A. Izatt, “Spectroscopic Optical Coherence Refraction Tomography”, , Optics Letters, 45(7), pp. 2091-2094, April 2020
  45. G. Song, Z.A. Steelman, S. Finkelstein, Z. Yang, L. Martin, K.K. Chu, S. Farsiu, V.Y. Arshavsky, A. Wax, “Multimodal Coherent Imaging of Retinal Biomarkers of Alzheimer's Disease in a Mouse Model”, , Scientific Reports, 13;10(1), pp.7912, May 2020
  46. X.D. Chen, A. Omari, M. Hwang, L. Kwark, N. Dakki, S. Farsiu, and T.W. Gardner, " “Treated Proliferative Diabetic Retinopathy Reveals Age-Appropriate Vision Deterioration But Distorted Retinal Organization”, Translational Vision Science and Technology,9(3), Feb. 2020
  47. E.N. Woertz, B.S. Omoba, T.M. Dunn, S.J. Chiu, S. Farsiu, S .Strul, C.G. Summers, A.V. Drack, J. Carroll, "Assessing Ganglion Cell Layer Topography in Human Albinism Using Optical Coherence Tomography", , Investigative Ophthalmology & Visual Science, 61(3):36, March 2020
  48. A. Hasan, J.M. Pereira, R.J. Ravier, S. Farsiu, V. Tarokh, “Learning Partial Differential Equations from Data Using Neural Networks", , in IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), pp. 3962-3966, May 2020.

    49. 2019

  49. D. Cunefare, A.L. Huckenpahler, E.J. Patterson, A. Dubra, J. Carroll, and S. Farsiu, " RAC-CNN: multimodal deep learning based automatic detection and classification of rod and cone photoreceptors in adaptive optics scanning light ophthalmoscope images", Biomedical Optics Express, 10(8), pp. 3815-3832, August 2019
  50. K.C. Zhou, R. Qian, S. Degan, S. Farsiu, and J.A. Izatt," Optical Coherence Rrefraction Tomography", Nature Photonics, 13, pp. 794–802, Nov. 2019 Open Source Software and Data,
  51. S. Soltanian-Zadeh , K. Sahingur , S. Blau, Y. Gong , and S. Farsiu,"Fast and Robust Active Neuron Segmentation in Two-photon Calcium Imaging using Spatio-temporal Deep-learning", Proceedings of the National Academy of Sciences (PNAS), 116(17), pp. 8554-8563, April 2019 PrePrint Open Source Software and Data, News
  52. T. DuBose, F. LaRocca, S. Farsiu, and J.A. Izatt. "Super resolution retinal imaging using optically reassigned scanning laser ophthalmoscopy” Nature Photonics, 13, pp.257–262, 2019
  53. K.J. McHugh, D. Li, J.C. Wang, L. Kwark, V. Macha, S. Farsiu, L.A. Kim, M. Saint-Geniez, "Computational modeling of retinal hypoxia and photoreceptor degeneration in patients with age-related macular degeneration", PlosOne, 14(6):e0216215, 2019
  54. S.S. Ong, A.D. Proia, H.E. Whitson, S. Farsiu, P.M. Doraiswamy, E.M. Lad, "Ocular Amyloid Imaging at the Crossroad of Alzheimer’s Disease and Age-Related Macular Degeneration: Implications for Diagnosis and Therapy", Journal of Neurology, 266(7), pp 1566–1577, July 2019
  55. E.Y. Chew, T.E. Clemons, G.J. Jaffe, C.A. Johnson, S. Farsiu, E.M. Lad, R. Guymer, P. Rosenfeld, J.P. Hubschman, I. Constable, H. Wiley, L.J. Singerman, M. Gillies, G. Comer, B. Blodi, D. Eliott, J. Yan, A. Bird, M. Friedlander, "Effect of Ciliary Neurotrophic Factor on Retinal Neurodegeneration in Patients with Macular Telangiectasia Type 2: A Randomized Clinical Trial", Ophthalmology, 126(4), pp. 540-549, April 2019
  56. D. Wang, S. Xu, P. Pant, E. Redington, S. Soltanian-Zadeh, S. Farsiu, and Y. Gong, “Hybrid light-sheet and light-field microscope for high resolution and large volume neuroimaging”, Biomedical Optics Express, 10(12), pp.6595-6710, Dec. 2019
  57. C.A. Toth, V. Tai, M. Pistilli, S. Chiu, K. Winter, E. Daniel, J. Grunwald, G. Jaffe, D. Martin, G. Ying, S. Farsiu, M. Maguire, "Distribution of OCT features within areas of macular atrophy or scar after two years of anti-VEGF treatment for neovascular AMD in CATT", Ophthalmology Retina, 3(4), pp. 316–325, April 2019
  58. M. Patel, D. Mukherjee, S. Farsiu, B. Munoz, A. B. Blood, C. G. Wilson, and J. B. Griffin. "Estimation of gestational age via image analysis of anterior lens capsule vascularity in preterm infants: a pilot study." Front. Pediatr. 7: 43. 2019.
  59. T.Alabduljalil, C.A. Westall, A. Reginald, S. Farsiu, S.J. Chiu, A. Arshavsky, C.A. Toth, W. Lam, " Demonstration of anatomical development of the human macula within the first 5 years of life using handheld OCT ", International Ophthalmology 39(7), pp 1533–1542, July 2019
  60. G. Yiu, V.S. Vuong, S. Tran, J. Migacz, D. Cunefare, S. Farsiu, N. Khandelwal, R. Agrawal, and C.M.G. Cheung, " Vascular Response to Sildenafil Citrate in Aging and Age-Related Macular Degeneration", Scientific Reports, 9:5049, March 2019
  61. G. Li, C. Lee, V. Agrahari, K. Wang, I. Navarro, J.M. Sherwood, K. Crews, S. Farsiu, P. Gonzalez, C.W. L, A. K. Mitra, C.R. Ethier, and W.D. Stamer, "In vivo measuremnet of trabecular meshwork stiffness in a novel corticosteroid-induced ocular hypertensive mouse model", Proceedings of the National Academy of Sciences (PNAS), 116(5), 1714-1722, Januray 2019

    62. 2018

  62. T. DuBose, D. Nankivil, F. LaRocca, G. Waterman, K. Hagan, J. Polans, B. Keller, D. Tran-Viet, L. Vajzovic, A.N. Kuo, C.A. Toth, J.A. Izatt, and S. Farsiu, "Handheld Adaptive Optics Scanning Laser Ophthalmoscope", Optica; 5 (9), pp. 1027-1037, Sept. 2018 Open Source Software, News
  63. A.D. Desai, C. Peng, L. Fang, D. Mukherji, A. Yeung, S.J. Jaffe, J.B. Griffin, and S. Farsiu, " Open-source, machine and deep learning based automated algorithm for gestational age estimation through smartphone lens imaging ", Biomedical Optics Express, 9(12), pp. 6038-6052, Dec. 2018, Open Source Software, News
  64. D. Cunefare, C.S. Langlo, E.J. Patterson, S. Blau, A. Dubra, J. Carrol, and S. Farsiu, " Deep learning based detection of cone photoreceptors with multimodal adaptive optics scanning light ophthalmoscope images of achromatopsia ", Biomedical Optics Express, 9(8), pp. 3740-3756, 2018
  65. J. Loo, L. Fang, D. Cunefare, G.J. Jaffe, and S. Farsiu, " Deep longitudinal transfer learning-based automatic segmentation of photoreceptor ellipsoid zone defects on optical coherence tomography images of macular telangiectasia type 2 ", Biomedical Optics Express,9(6), pp. 2681-2698, 2018
  66. S. Soltanian-Zadeh, Y. Gong, and S. Farsiu, "Information-Theoretic Approach and Fundamental Limits of Resolving Two Closely-Timed Neuronal Spikes in Mouse Brain Calcium Imaging", IEEE Transactions on Biomedical Engineering ;65 (11), pp. 2428-2439, Nov. 2018 Open Source Software (PREPRINT PDF)
  67. T.B. DuBose, D. Cunefare, E. Cole, P. Milanfar, J.A. Izatt, and S. Farsiu, "Statistical Models of Signal and Noise and Fundamental Limits of Segmentation Accuracy in Retinal Optical Coherence Tomography", IEEE Transactions on Medical Imaging ; 37(9), pp. 1978 - 1988, Sept. 2018 Open Source Software (PREPRINT PDF)
  68. Z. Smit-McBride, J. Nguyen, G.W. Elliott, Z. Wang, R.A. McBride, A.T. Nguyen, S.L. Oltjen, G. Yiu, S.M. Thomasy, K.E. Pinkerton, E.S. Lee, D. Cunefare, S. Farsiu, L.S. Morse, "Effects of aging and environmental tobacco smoke exposure on ocular and plasma circulatory microRNAs in the Rhesus macaque", Molecular Vision , 24:633-646, 2018
  69. E.M. Lad, D. Mukherjee, S.S. Stinnett, S.W. Cousins, G.G. Potter, J.R. Burke, S. Farsiu, H.E. Whitson, "Evaluation of inner retinal layers as biomarkers in mild cognitive impairment to moderate Alzheimer’s disease", PlosOne , 13(2): e0192646, 2018
  70. B. Keller, M. Draelos, G. Tang, S. Farsiu, A.N. Kuo, K. Hauser, and J.A. Izatt, "Real-time Corneal Segmentation and 3D Needle Tracking in Intrasurgical OCT", Biomedical Optics Express,9(6), pp. 2716-2732, June 2018
  71. A.S. Willoughby, V. S. Vuong, D. Cunefare, S. Farsiu, G. Noronha, R.P. Danis, G. Yiu, "Choroidal Changes after Suprachoroidal Injection of Triamcinolone in Eyes with Macular Edema Secondary to Retinal Vein Occlusion", American Journal of Ophthalmology ,146, pp. 144-151, Feb. 2018
  72. C.A. Toth, V. Tai, S.J. Chiu, K. Winter, M.B. Sevilla, E. Daniel, J.E. Grunwald, G.J. Jaffe, D.F. Martin, G. Ying, M. Pistilli, S. Farsiu, M.G. Maguire, " Linking OCT, Angiographic, and Photographic Lesion Components in Neovascular Age-Related Macular Degeneration ", Ophthalmology Retina, 2(5), pp. 481-495, May 2018
  73. T.P. Patel, N.V. Prajna, S. Farsiu, N.G. Valikodath, L. Dudeja, L.M. Niziol, K.H. Kim, M.A. Woodward; “Novel image-based analysis for reduction of clinician-dependent variability in measurement of corneal ulcer size”, Cornea. 37(3), pp. 331-339 March 2018.
  74. A. Gibson, K.E. Piquette, U. Bergmann, W. Christens-Barry, G. Davis, M. Endrizzi, S. Fan, S. Farsiu, A. Fitzgerald, J. Griffiths, C. Jon, G. Li, P.L. Manning, C.M. Jones, R. Mazza, D. Mills, P. Modregger, P.R.T. Munro, A. Olivo, A. Stevenson, B. Venugopal, V. Wallace, R.A. Wogelius, M.B. Toth and M. Terras"An assessment of multimodal imaging of subsurface text in mummy cartonnage using surrogate papyrus phantoms". Heritage Science, 6:7, 2018
  75. G. Yiu, Z. Wang, C. Munevar, E. Tieu, B. Shibata, B. Wong, D. Cunefare, S. Farsiu, J. Roberts, S. Thomasy, “ Comparison of Chorioretinal Layers in Rhesus Macaques using Spectral-Domain Optical Coherence Tomography and High-Resolution Histological Sections ”, Experimental Eye Research, 168, pp.69-78, March 2018

    76. 2017

  76. D. Cunefare, L. Fang, R.Cooper, A. Dubra, J. Carroll, and S. Farsiu, "Open source software for automatic detection of cone photoreceptors in adaptive optics ophthalmoscopy using convolutional neural networks", Scientific Reports, 7(1):6620, July 2017 Software and Dataset
  77. D. Mukherjee, E. Lad, R. R. Vann, S.J. Jaffe, T.E. Clemons, M. Friedlander, E.Y. Chew, G. Jaffe, and S. Farsiu, "Correlation Between Macular Integrity Assessment and Optical Coherence Tomography Imaging of Ellipsoid Zone in Macular Telangiectasia Type 2", Investigative Ophthalmology & Visual Science ; 58(6):BIO291-BIO299, Sept. 2017
  78. L. Fang, D. Cunefare, C. Wang, R.H. Guymer, S. Li, and S. Farsiu, "Automatic Segmentation of Nine Retinal Layer Boundaries in OCT Images of Non-exudative AMD Patients using Deep Learning and Graph Search", Biomedical Optics Express, 8(5), pp. 2732-2744, May. 2017
  79. L. Fang, S. Li, D. Cunefare, S. Farsiu, "Segmentation Based Sparse Reconstruction of Optical Coherence Tomography Images ", IEEE Transactions on Medical Imaging , 36(2), pp. 407-412, Feb.2017, Software
  80. J. Polans, D. Cunefare, E. Cole, B. Keller, P.S. Mettu, S.W. Cousins, M.J. Allingham, J.A. Izatt, and S. Farsiu, "Enhanced Visualization of Peripheral Retinal Vasculature with Wavefront Sensorless Adaptive Optics OCT Angiography in Diabetic Patients", Optics Letters , 42(1), pp.17-20, 2017
  81. M. J. Allingham, D. Mukherjee, E.B. Lally, H. Rabbani, P.S. Mettu , S.W. Cousins, S. Farsiu, "A quantitative approach to predict differential effects of anti-VEGF treatment on diffuse and focal leakage in patients with diabetic macular edema - a pilot study",Translational Vision Science & Technology ;6,7, March 2017
  82. K. Sleiman, M. Veerappan, K.P. Winter, M.N. McCall, G. Yiu, S. Farsiu, E.Y. Chew, T. Clemons, C.A. Toth; “Optical Coherence Tomography Predictors of Risk for Progression to Non-Neovascular Atrophic Age-Related Macular Degeneration”, Ophthalmology. 124(12), pp.1764-1777, Dec. 2017
  83. R. Qiana, O.M. Carrasco-Zevallosa, S. Mangaleshb, N.  Sarin, L. Vajzovic, S. Farsiu, J. A. Izatt, C. A. Toth, “Characterization of Long Working Distance Optical Coherence Tomography for Imaging of Pediatric Retinal Pathology”,Translational Vision Science & Technology 6(12), 2017
  84. S.G. Prakalapakorn, L.A. Vickers, R. Estrada, S.F. Freedman, C. Tomasi, S. Farsiu, and D.K. Wallace, “Using an Image Fusion Methodology to Improve Efficiency and Traceability of Posterior Pole Vessel Analysis by ROPtool”, Open Ophthalmology Journal 11, 143-151, June 2017
  85. G. Yiu, E. Tieu, C. Munevar, B. Wong, D. Cunefare, S. Farsiu, L. Garzel, J. Roberts, S. Thomasy, “ In Vivo Multimodal Imaging of Drusenoid Lesions in Rhesus Macaques”, Scientific Reports, 7(1):15013, Nov. 2017
  86. R.P. McNabb, J. Tian, S. Farsiu, J.A. Izatt, E.M. Lad, and A. N. Kuo, "Retinal imaging in human autopsy eyes using a custom optical coherence tomography periscope", Biomedical Optics Express, 8(9), 4152-4159, Sept 2017
  87. S.S. Wong, V.S. Vuong, D. Cunefare, S. Farsiu, A. Moshiri, G. Yiu, "Macular fluid reduces reproducibility of choroidal thickness measurements on enhanced depth optical coherence tomography", American Journal of Ophthalmology, 184, pp. 108-114, Dec. 2017
  88. J. Polans, B. Keller, O. Carrasco-Zevallos, F. LaRocca, E. Cole, H.E. Whitson, E.M. Lad, S. Farsiu, and J.A. Izatt "Wide-field retinal optical coherence tomography with wavefront sensorless adaptive optics for enhanced imaging of targeted regions", Biomedical Optics Express ,8(1),pp. 16-37, Jan. 2017
  89. J. Wang, M.L. O’Sullivan, D. Mukherjee, S. Farsiu, J. N. Kay, " Anatomy and spatial organization of Muller glia in mouse retina ", Journal of Comparative Neurology, 525(8),: 1759 –1777, 2017 Software
  90. A.S. Willoughby, S.J. Chiu, R.K. Silverman, S. Farsiu, C. Bailey, H.E. Wiley, F.L. Ferris, III, G. J. Jaffe, "Platform-Independent Cirrus and Spectralis Thickness Measurements in Eyes with Diabetic Macular Edema Using Fully Automated Software " Translational Vision Science & Technology ;6(1):9, Feb. 2017

    91. 2016

  91. D. Cunefare, R.F. Cooper, B. Higgins, D.F. Katz, A. Dubra, J. Carroll, S. Farsiu, "Automatic detection of cone photoreceptors in split detector adaptive optics scanning light ophthalmoscope images", Biomedical Optics Express , pp. 2036-2050, May 2016
  92. F. LaRocca, D. Nankivil, T. DuBose, C. A. Toth, S. Farsiu, and J. A. Izatt, "In vivo cellular resolution retinal imaging in infants and children using an ultra-compact handheld probe ", Nature Photonics ,10, 580-584, 2016
  93. J. Lezama, D. Mukherjee, R.P. McNabb, G. Sapiro, A.N. Kuo, S. Farsiu, "Segmentation guided registration of wide field-of-view retinal optical coherence tomography volumes ", Biomedical Optics Express ,7(12), 4827-4846, Dec. 2016 Software
  94. J. Simonett, R. Huang, N. Siddique, S. Farsiu, T. Siddique, N. Volpe, and A. Fawzi, "Macular sub-layer thinning and association with pulmonary function tests in Amyotrophic Lateral Sclerosis ", Scientific Reports, 6, 29187, 2016
  95. O. Carrasco-Zevallos, B. Keller, C. Viehland, L. Shen, G. Waterman, B Todorich, C. Shieh, P. Hahn, S. Farsiu, A.N. Kuo, C.A. Toth, J.A. Izatt, "Live volumetric (4D) visualization and guidance of in vivo human ophthalmic surgery with intraoperative optical coherence tomography ", Scientific Reports,  6, 31689, 2016
  96. Z. Wu, D. Cunefare , E. Chiu, C.D. Luu, L.N. Ayton , C.A. Toth, S. Farsiu*, R.H. Guymer** [*,**Both authors contributed equally as senior authors], "Longitudinal Associations Between Microstructural Changes and Microperimetry in the Early Stages of Age-Related Macular Degeneration ", IOVS , 57(8), pp.3714-3722 , July 2016
  97. B. Keller, D. Cunefare, D. Grewal, T. Mahmoud, J.A. Izatt, S. Farsiu, "Length-Adaptive Graph Search for Automatic Segmentation of Pathological Features in OCT Images", Journal of Biomedical Optics, 21(7),pp. 076015 July 2016 SOFTWARE
  98. B. Knoll, J. Simonett, N.J. Volpe, S. Farsiu, M. Ward, A. Rademaker, S. Weintraub, A.A. Fawzi, " Retinal nerve fiber layer thickness in amnestic mild cognitive impairment: Case-control study and meta-analysis ", Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring, 4, pp. 85–93, 2016
  99. B. Todorich, C. Shieh, P. J. DeSouza, O. M Carrasco-Zevallos, D. Cunefare, S. S. Stinnett, J.A. Izatt, S. Farsiu, P. Mruthyunjaya, A.N. Kuo, C. A Toth, " Impact of Microscope-Integrated OCT on Ophthalmology Resident Performance of Anterior Segment Surgical Maneuvers in Model EyesImpact of MI-OCT on Ophthalmology Resident Performance ", Investigative Ophthalmology & Visual Science, 57(9), pp. OCT146-OCT153, July 2016
  100. G.Yiu, V. Vuong, S. Oltjen, D. Cunefare, S. Farsiu, L. Garzel, J. Roberts, S. Thomasy, "Effect of Uveal Melanocytes on Choroidal Morphology in Rhesus Macaques and Humans on Enhanced-Depth Imaging Optical Coherence Tomography ", Investigative Ophthalmology & Visual Science, 57 (13), pp. 5764-5771, Oct. 2016
  101. N. Pasricha, C. Shieh, O. Carrasco-Zevallos, B. Keller, D. Cunefare, J. Mehta, S. Farsiu, J. Izatt, C. Toth, A. Kuo, "Needle Depth and Big Bubble Success in Deep Anterior Lamellar Keratoplasty: An Ex Vivo Microscope-Integrated OCT Study " Cornea , 35(11), p 1471–1477, November 2016
  102. M.D. Twa, K.L. Schulle, S.J. Chiu, S. Farsiu, D.A. Berntsen, "Validation of Automated Choroidal Thickness Measurements from SD-OCT", Optometry and Vision Science , 93(11), pp. 1387-1398. Nov. 2016
  103. G. Li, D. Mukherjee, I. Navarro, N.E. Ashpole, J.M. Sherwood, J. Chang, D.R. Overby, F. Yuan, P. Gonzalez, C.C. Kopczynski, S. Farsiu, W.D. Stamer, "Visualization of conventional outflow tissue responses to netarsudil in living mouse eyes",European Journal of Pharmacology, 787(15) 20–31, Sept. 2016
  104. M.J. Allingham, Q. Nie, E.M. Lad, D.J. Izatt, P.S. Mettu, S.W. Cousins, S. Farsiu, "Semiautomatic Segmentation of Rim Area Focal Hyperautofluorescence Predicts Progression of Geographic Atrophy Due to Dry Age-Related Macular Degeneration ", IOVS,57(4), pp. 2283-9, Apr. 2016
  105. V.S. Vuong, E. Moisseiev, D. Cunefare, S. Farsiu, A. Moshiri, G. Yiu, "Repeatability of Choroidal Thickness Measurements on Enhanced Depth Imaging Optical Coherence Tomography Using Different Posterior Boundaries ", American Journal of Ophthalmology ,169, pp.104-112, Sept. 2016
  106. A.N. Kuo, P.K. Verkicharla, R.P.McNabb, C.Y. Cheung, S. Hilal, S.Farsiu, C. Chen, T.Y.Wong, M.K. Ikram, C.Y. Cheng, T.L. Young, S. M. Saw, J.A. Izatt, " Posterior Eye Shape Measurement With Retinal OCT Compared to MRI " Investigative Ophthalmology & Visual Science , 57(9), pp. 196-203, July 2016
  107. M.B. Sevilla, G. McGwin, E.M. Lad, M. Clark, E.L. Yuan, S. Farsiu, C.A. Curcio, C. Owsley, C.A. Toth, "Relating Retinal Morphology and Function in Aging and Early to Intermediate Age-related Macular Degeneration Subjects ", American journal of ophthalmology ,165, pp. 65-77, May, 2016
  108. M.S. Stem, G.E. Boynton, G.R. Jackson, S. Farsiu, R. Pop-Busui, T.W. Gardner, "Glucose Variability and Inner Retinal Sensory Neuropathy in Persons with Type 1 Diabetes Mellitus", Eye.,30(6), pp. 825-832, 2016
  109. S. Kim, S. Heflin, L.A. Kresty, M. Halling, L.N. Perez, D. Ho, M. Crose, W. Brown, S. Farsiu, V. Arshavsky, and A. Wax, "Analyzing spatial correlations in tissue using angle-resolved low coherence interferometry measurements guided by co-located optical coherence tomography", Biomed. Opt. Express ,7(4), pp. 1400-1414, 2016
  110. F.A. Folgar, MD; E.L. Yuan, M.B. Sevilla, S.J. Chiu, S. Farsiu; E.Y. Chew, C.A. Toth, Drusen volume and retinal pigment epithelium abnormal thinning volume predict 2-year progression of age-related macular degeneration, Ophthalmology 123(1), pp. 39-50, 2016
  111. C. Bavinger, G. Boynton, M. Stem, T. Blachley, L. Kwark, S. Farsiu, G. Jackson, and T. Gardner, "The effects of diabetic retinopathy and pan-retinal photocoagulation on photoreceptor cell function as assessed by dark adaptometry", IOVS , 57(1), pp.208-2117 , Jan 2016

    112. 2015

  112. R. Estrada, C. Tomasi, S.C. Schmidler, and S. Farsiu, "Tree Topology Estimation", IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 37(8),pp. 1688-1701 August 2015 DATASET
  113. S.J. Chiu, M.J. Allingham, P.S. Mettu, S.W. Cousins, J.A. Izatt, S. Farsiu, "Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema" , Biomedical Optics Express, 6(4), pp. 1172-1194, April 2015 DATASET
  114. L. Fang, S. Li, X. Kang, J.A. Izatt, and S. Farsiu, "3-D Adaptive Sparsity Based Image Compression with Applications to Optical Coherence Tomography", IEEE Transactions on Medical Imaging, 34(6), 1306 - 1320, June 2015
  115. H. Rabbani, M.J. Allingham, P.S. Mettu, S.W. Cousins, S. Farsiu, "Fully Automatic Segmentation of Fluorescein Leakage in Subjects with Diabetic Macular Edema", Investigative Ophthalmology and Visual Science, 56(3) 1482-1492, March 2015 DATASET
  116. R. Estrada, M.J. Allingham, P.S.. Mettu, S.W. Cousins, C. Tomasi, and S. Farsiu, ""Retinal Artery-Vein Classification via Topology Estimation",IEEE Transactions on Medical Imaging, 34(12):2518-34 Dec. 2015 DATASET
  117. R.P. McNabb, S. Farsiu, S.S. Stinnett, A.N. Kuo, J.A. Izatt, "Optical Coherence Tomography Accurately Measures Corneal Power Change Post Laser Refractive Surgery ",Ophthalmology 122(4), Pages 677-686, April 2015
  118. G. Yiu, S.J. Chiu, P. A. Petrou, S. Stinnett, N. Sarin, S. Farsiu, E. Y. Chew, W. T. Wong, C.A. Toth "Relationship of Central Choroidal Thickness with Age-Related Macular Degeneration Status ", American Journal of Ophthalmology ;159(4):617-626, Apr2015

  119. B.E. Goldhagen, M.D.; M. T. Bhatti, P.P. Srinivasan, S.J. Chiu, S. Farsiu, M. Al-Dairi,"Subclinical Retinal Atrophy in Eyes with Resolved Papilledema Detected by Optical Coherence Tomography ", Journal of Neuro-Ophthalmology , 35(2):122-126, June, 2015
  120. G. E. Boynton; M. S. Stem; L. Kwark; G.R. Jackson; S. Farsiu; T.W. Gardner "Multimodal Characterization of Proliferative Diabetic Retinopathy Reveals Alterations in Outer Retinal Function and Structure", Ophthalmology, 122(5):957-967, May, 2015
  121. D.H. Nam, P.J. Desouza, P. Hahn, V. Tai, M.B. Sevilla, D. Tran-Viet, D. Cunefare, S. Farsiu, J.A. Izatt, C.A. Toth, Intraoperative spectral-domain optical coherence tomography imaging after internal limiting membrane peeling in idiopathic epiretinal membrane with connecting strands, Retina, 35(8):1622-1630, August 2015
  122. A.L. Rothman, M.B. Sevilla, S.F. Freedman, A.Y. Tong, V. Tai, D. Tran-Viet, S. Farsiu, C.A. Toth,M. El-Dairi " Assessment of Retinal Nerve Fiber Layer Thickness in Healthy, Full-Term Neonates" American Journal of Ophthalmology, 159(4):803-811 April, 2015
  123. P. Hahn; O. Carrasco-Zevallos; D. Cunefare; J. Migacz;S. Farsiu; J.A. Izatt; C.A. Toth, " Intrasurgical human retinal and instrument imaging with trackingusing a microscope-integrated spectral domain optical coherence tomography device", Translational Vision Science & Technology, 4(1), pp. 1-9, July 2015
  124. A. Boussommier-Calleja, G. Li, A. Wilson, T. Ziskind, O. Elena, N.E. Ashpole, J.M. Sherwood, S. Farsiu, P. Challa, P. Gonzalez, J. Downs, C. Ethier, W. Stamer, and D. Overby, "Physical Factors Affecting Outflow Facility Measurements in Mice ", IOVS, 56(13), pp. 8331-9, Dec. 2015

    125. 2014

  125. S. Farsiu, SJ. Chiu, R.V. O'Connell, F.A. Folgar, E. Yuan, J.A. Izatt, and C.A. Toth, "Quantitative Classification of Eyes with and without Intermediate Age-related Macular Degeneration Using Optical Coherence Tomography", Ophthalmology 121(1), 162-172 January (2014)(Download Complete Study Datase and Results)
  126. P. P. Srinivasan, L.A. Kim, P.S. Mettu, S.W. Cousins, G.M. Comer, J.A. Izatt, and S. Farsiu,; "Fully automated detection of diabetic macular edema and dry age-related macular degeneration from optical coherence tomography images ", Biomedical Optics Express, 5(10), pp. 3568-3577, Oct. 2014 DATASET

  127. J. Polans, R.P. McNabb, J. A. Izatt, and S. Farsiu, "Compressed Wavefront Sensing", Optics Letters, 39(5), 1189-1192, March 2014 Download Complete Study Dataset, Results, and Software.
  128. P.P. Srinivasan, S.J. Heflin, J.A. Izatt, V.Y. Arshavsky,and S. Farsiu, ""Automatic segmentation of up to ten layer boundaries in SD-OCT images of the mouse retina with and without missing layers due to pathology"", Biomedical Optics Express, 5(2), pp.348-365, Feb. 2014
  129. G. Yiu , P. Pecen , N. Sarin , S. Chiu , S. Farsiu , P. Mruthyunjaya , C. Toth , Characterization of the Choroid-Scleral Junction and Suprachoroidal Layer in Healthy Subjects on Enhanced-Depth Imaging Optical Coherence Tomography, JAMA Ophthalmology, 132(2):174-181, February 2014
  130. F. LaRocca, D. Nankivil, S. Farsiu, J.A. Izatt, " True color scanning laser ophthalmoscopy and optical coherence tomography handheld probe", Biomedical Optics Express 5 (9), pp.3204-3216, August 2014
  131. G. Li , S. Farsiu , P. Gonzalez, E. Lutjen-Drecoll, D. R. Overby, and W. D. Stamer, "Pilocarpine-induced dilation of Schlemm's canal and prevention of lumen collapse at elevated intraocular pressures in living mice visualized by OCT ", Investigative Ophthalmology & Visual Science, 55(6), pp. 3737-3746, June 2014 (High-resolution PDF 46MB)
  132. G. Yiu, V. Manjunath, S.J. Chiu, S. Farsiu, T. Mahmoud "Effect of Anti-VEGF Therapy on Choroidal Thickness in Diabetic Macular Edema", American Journal of Ophthalmology, 158(4), pp. 745-751.e2 October 2014
  133. D.k Nankivil, A.H. Dhalla, N. Gahm, K. Shia, S. Farsiu , and J.A. Izatt, �Coherence Revival Multiplexed, Buffered Swept Source Optical Coherence Tomography: 400kHz Imaging with a 100kHz Source� Optics Letters, 39(13), pp. 3740-3743, July 2014.

  134. F. Folgar, E. Yuan, S. Farsiu, and C. Toth, "Axial and lateral measurement differences between spectral domain optical coherence tomography systems", Journal of Biomedical Optics,19(1), 016014, Jan. 2014

  135. G. Li, S. Farsiu, J. Qiu, A. Dixon, C. Song, S. McKinnon, F. Yuan, P. Gonzalez, and W. Stamer "Disease progression in iridiocorneal angle tissues by optical coherence tomography in BMP2-induced ocular hypertensive mice", Molecular Vision, 20, pp. 1695-1709, December 2014

    136. 2013

  136. L. Fang, S. Li, R. P. McNabb, Q. Nie, A. N. Kuo, C. A. Toth, J. A. Izatt, and S. Farsiu, "Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation", IEEE Transactions on Medical Imaging, 32(11), pp. 2034 - 2049 Nov. 2013 Download Complete Study Dataset, Results, and Software.

  137. J.Y. Lee, S.J. Chiu, P.P. Srinivasan, J.A. Izatt, C.A.Toth, S. Farsiu, G.J. Jaffe, "Fully Automatic Software for Quantification of Retinal Thickness and Volume in Eyes with Diabetic Macular Edema from Images Acquired by Cirrus and Spectralis Spectral Domain Optical Coherence Tomography Machines" , Investigative Ophthalmology & Visual Science 54(12) pp. 7595-7602, Nov.2013
  138. S.J. Chiu, Y.V. Lokhnygina, A.M. Dubis, A. Dubra, J. Carroll, J. A. Izatt, and S. Farsiu, Automatic cone photoreceptor segmentation using graph theory and dynamic programming, Biomedical Optics Express, 4(6), pp. 924-937 (2013). DATASET
  139. F. LaRocca, D. Nankivil, S. Farsiu, J.A. Izatt, "Handheld simultaneous scanning laser ophthalmoscopy and optical coherence tomography system", Biomedical Optics Express, 4(11),pp. 2307-2321, Nov. 2013
  140. C. Bowes Rickman, S. Farsiu, C.A. Toth, M. Klingeborn, "Dry age-related macular degeneration: Mechanisms, therapeutic targets and imaging", Investigative Ophthalmology & Visual Science ;54(14): 68-80, Dec. 2013.

  141. F. LaRocca, A.H. Dhalla, M.P. Kelly, S. Farsiu, J.A. Izatt, Optimization of confocal scanning laser ophthalmoscope design, Journal of Biomedical Optics, 18(7), 076015(1-9) July 2013
  142. H.C. Hendargo, R. Estrada, S.J. Chiu, C. Tomasi, S. Farsiu, and J.A. Izatt , Automated non-rigid registration and mosaicing for robust imaging of distinct retinal capillary beds using speckle variance optical coherence tomography, Biomedical Optics Express, 4(6), pp. 803-821, June 2013
  143. M.T Cabrera, R.V O'Connell, C.A. Toth, R.S. Maldonado, D. Tran-Viet, M.J. Allingham, S.J. Chiu, S. Farsiu, D.K. Wallace, G.M.M. Panayotti, G.K. Swamy,S.F. Freedman, Macular findings in healthy full term Hispanic newborns observed by hand-held Spectral Domain Optical Coherence Tomography,Ophthalmic Surgery, Lasers and Imaging Retina, 44(5), pp. 448-454, September 2013
  144. A. N. Kuo, R. P. McNabb, S.J. Chiu, M. Al-Dairi, S. Farsiu, C.A. Toth, and J. A. Izatt, "Correction of ocular shape in retinal optical coherence tomography and effect on current clinical measures", American Journal of Ophthalmology, 156(2), Pages 304-311, August 2013.
  145. T.A. Moreno, R.V. O'Connell , S.J. Chiu , S. Farsiu , M.T. Cabrera , R. Maldonado , D. Tran-Viett , S. F. Freedman , D.K. Wallace, "Choroid Development and Feasibility of Choroidal Imaging in the Preterm and Term Infants Utilizing SD-OCT.", Investigative Ophthalmology & Visual Science ;54(6):4140-7, June, 2013.
  146. J.G. Christenbury; F.A Folgar, R. V. O'Connell, S.J. Chiu, S. Farsiu, C.A. Toth,, "Progression of intermediate AMD with proliferation and inner retinal migration of hyperreflective foci", Ophthalmology ;120(5):1038-45 , May 2013
  147. J. P. Ehlers, K. Tao, S. Farsiu, R. Maldonado, J.A. Izatt, C.A. Toth ,Visualization of Real-time Intraoperative Maneuvers with a Microscope Mounted Spectral Domain Optical Coherence Tomography System, Retina. ;33(1):232-6. Jan 2013.

    148. 2012

  148. L. Fang, S. Li, Q. Nie, J.A. Izatt, C.A. Toth, and S. Farsiu, "Sparsity Based Denoising of Spectral Domain Optical Coherence Tomography Images", Biomedical Optics Express , 3(5), pp. 927-942, May, 2012 Download Complete Study Datase, Results, and Software. .News
  149. R. P. McNabb, F. LaRocca, S. Farsiu, A. N. Kuo, and J. A. Izatt, "Distributed Scanning Volumetric SDOCT for Motion Corrected Corneal Biometry", Biomedical Optics Express, 3(9), 2050-2065, Sept.,(2012) .

  150. A. Kuo, R. McNabb, M. Zhao, F. LaRocca, S. Stinnett, S. Farsiu, and J. Izatt, "Corneal Biometry from Volumetric SDOCT Data and Comparison with Existing Clinical Modalities", Biomedical Optics Express, 3(6), pp. 1279-1290, June, 2012.
  151. S. J. Chiu, C. A. Toth, C. Bowes Rickman, J.A. Izatt, S. Farsiu. "Automatic Segmentation of Closed Contour Features in Ophthalmic Images using Graph Theory and Dynamic Programming", Biomedical Optics Express, Vol. 3, Issue 5, pp. 1127-1140. May 2012 Download Complete Study Dataset Including our Automated and Manual Markings
  152. R. Estrada, C. Tomasi, M. T. Cabrera, D.K. Wallace, S.F. Freedman, S. Farsiu. "Exploratory Dijkstra forest based automatic vessel segmentation: applications in video indirect ophthalmoscopy (VIO)",Biomedical Optics Express, 3(2), pp. 327-339 Feb. 2012. Download Software (MATLAB Code)
  153. S.J. Chiu, J.A. Izatt, R.V. O'Connell, K.P. Winter, C.A. Toth, S. Farsiu, "Validated Automatic Segmentation of AMD Pathology including Drusen and Geographic Atrophy in SDOCT Images", Investigative Ophthalmology & Visual Science, 53(1), pp. 53-61, Jan. 2012. Complete Study Dataset Including our Automated and Manual Markings
  154. P. Lin, P.S. Mettu, D.L. Pomerleau, S.J. Chiu, R. Maldonado, S. Stinnett, C. Toth, S. Farsiu, P.Mruthyunjaya, Image inversion on spectral-domain optical coherence tomography optimizes choroidal thickness measurement and visualization of outer choroidal detail through improved outer choroidal contrast,Investigative Ophthalmology & Visual Science, 53(4), April, pp.1874-1882 2012.
  155. L. Vajzovic, A. Hendrickson, R.V. O'Connell, L.A. Clark, D. Tran-Viet, D. Possin, S.J. Chiu, S. Farsiu, C.A. Toth, "Maturation of the Human Fovea 2. Correlation of Spectral Domain Optical Coherence Tomography Findings with Histology", American Journal of Ophthalmology ;154(5):779-789, Nov. 2012.

  156. F. A. Folgar, J.H. Chow. W.T. Wong, S. Farsiu, S.G. Schuman, R. V. O'Connell, K.P. Winter, M. N. McCall, E.Y. Chew, T.S. Hwang, S.K. Srivastava, M. W. Harrington, T. E. Clemons, C.A. Toth, "Spatial correlation between hyperpigmentary changes on color fundus photography and hyperreflective foci on SD-OCT in intermediate AMD", Investigative Ophthalmology & Visual Science, 53(8), pp.4626-4633 , July 2012.
  157. R.S. Maldonado, R.V. O'Connell, S. Ascher, N. Sarin, S.F. Freedman, D.K. Wallace, S. J. Chiu, S. Farsiu, M.Cotten, C. A. Toth, "Spectral Domain Optical Coherence Tomography Assessment of Cystoid Macular Edema Severity in Retinopathy of Prematurity", Archives of Ophthalmology, 130(5):569-78. May2012.
  158. S. Yanni, J. Wang, M. Chan, J. Carroll, S. Farsiu, J. Leffler, R. Spencer, and E. Birch, Foveal Avascular Zone and Foveal Pit Formation After Preterm Birth, British Journal of Ophthalmology, 96 (7), Pages: 961-6 July 2012.
  159. M.T Cabrera, R.S. Maldonado, C.A. Toth, R.V O'Connell, B.B. Chen, S.J. Chiu, S. Farsiu, D.K. Wallace, G.M.M. Panayotti, G.K. Swamy,S.F. Freedman, "Subfoveal fluid in healthy full term newborns observed by hand held Spectral Domain Optical Coherence Tomography", American Journal of Ophthalmology, 153(1), 167-175, Jan. 2012

    160. 2011

  160. R. Estrada, C. Tomasi, M. T. Cabrera, D.K. Wallace, S.F. Freedman, S. Farsiu. "Enhanced Video Indirect Ophthalmoscopy (VIO) via Robust Mosaicing.BioMedical Optics Express, Vol. 2, Iss. 10, pp. 2871-2887, Oct. 2011.
  161. R.S. Maldonado, R.V. O'Connell, N. Sarin, S.F. Freedman, D.K. Wallace, M.Cotten, K.P. Winter,S.Stinnett, S.J. Chiu, J. A. Izatt, S. Farsiu, C. A. Toth, "Dynamics of Human Foveal Development after Premature Birth", Ophthalmology, 118(12):2315-25 Dec. 2011.
  162. J. P. Ehlers, K. Kernstine, S. Farsiu, N. Sarin, R. Maldonado, C.A. Toth, "Real-time Analysis of Pars Plana Vitrectomy for Optic Pit-related Maculopathy: A Connection with the Vitreous Cavity, Archives of Ophthalmology,129(11):pp. 1483-1486. Nov. 2011
  163. J. Ding, L. Johnson R. Herrmann, S. Farsiu, S. Smith, M. Groelle, B. Mace, P .Sullivan, J. Jamison, U. Kelly, Ons Harrabi, S. Bollini, J. Dilley, D. Kobayashi, B. Kuang, W. Li, J. Pons, J. Lin, C. Bowes Rickman, "Anti-amyloid immunotherapy protects against RPE damage and loss of visual function in a mouse model of age-related macular degeneration", Proceedings of the National Academy of Sciences (PNAS). 108 (28) 11307-11308, June, 2011. (full text in PNAS Plus PNAS | July 12, 2011 | vol. 108 | no. 28 | E279-E287)
  164. F. LaRocca, S.J. Chiu, R. McNabb, A.N. Kuo, J.A. Izatt, S. Farsiu, "Robust Automatic Segmentation of Corneal Layer Boundaries in SDOCT Images using Graph Theory and Dynamic Programming", BioMedical Optics Express, 2(6), pp. 1524-1538 (2011) .
  165. J. P. Ehlers, K. Tao, S. Farsiu, R. Maldonado, J.A. Izatt, C.A. Toth ,"Integration of a Spectral Domain Optical Coherence Tomography System into a Surgical Microscope for Intraoperative Imaging", Investigative Ophthalmology & Visual Science, 52 (6), pp. 3153-3159, May, 2011.
  166. B. Reidel, J. W. Thompson, S. Farsiu, M. A. Moseley, N. P. Skiba, V. Y. Arshavsky, "Proteomic mapping of the retina: A novel approach to label-free quantitative protein profiling of layered tissues",Molecular and Cellular Proteomics 10 (3) : M110.002469, March, 2011.

    167. 2010

  167. M.D. Robinson, C.A. Toth, J.Y. Lo, S. Farsiu, "Efficient Fourier-wavelet Super-resolution", IEEE Transactions on Image Processing, Vol 19, Issue 10, pp. pp. 2669 - 2681, October 2010.News
  168. J. P. Ehlers, P. K. Gupta, S. Farsiu, R. Maldonado, T. Kim, C.A. Toth, P. Mruthyunjaya,"Evaluation of Contrast Agents for Enhanced Visualization in Optical Coherence Tomography", Investigative Ophthalmology & Visual Science, 51(12),pp. 6614-6619, November 2010.
  169. Jain N, Farsiu S., Khanifar A, Bearelly S, Smith RT, Izatt J, Toth C, " Quantitative Comparison of Drusen Segmented on SD OCT versus Drusen Delineated on Color Fundus Photographs, ", Investigative Ophthalmology & Visual Science, vol. 51, no. 10, pp.4875-4883. October, 2010.
  170. Y.K. Tao, S. Farsiu, J.A. Izatt, Interlaced spectrally encoded confocal scanning laser ophthalmoscopy and spectral domain optical coherence tomography, Biomedical Optics Express, Vol. 1, Issue 2, pp. 431-440 September 2010.

  171. S.J. Chiu, X.T. Li, P. Nicholas, C.A. Toth, J.A. Izatt, S. Farsiu. Automatic Segmentation of Seven Retinal Layers in SDOCT Images Congruent with Expert Manual Segmentation. Optics Express. Vol. 18, No. 18, pp. 19413-19428, August 2010.

    172. 2009

  172. Chou N, Izatt JA, Farsiu S, "Generalized Pseudo-Polar Fourier Grids and Applications in Registering Ophthalmic Optical Coherence Tomography Images", Proc. Of the 43stAsilomar Conference on Signals, Systems, and Computers. Pacific Grove, CA. Nov. 2009.
  173. Chavala SH, Farsiu S, Maldonado R., Wallace D.K., Freedman S.F., Toth C.A., Insights into Advanced Retinopathy of Prematurity Utilizing Handheld Spectral Domain Optical Coherence Tomography Imaging, Ophthalmology, 116(12) Dec. 2009. Page(s): 2448-56
  174. Dayani P, Maldonado R., Farsiu S., Toth C., Intraoperative Use of Hand-held Spectral Domain Optical Coherence Tomography Imaging in Macular Surgery, Retina, 29(10) Nov. 2009. Page(s): 1457-68.
  175. Wang X., Farsiu S, Shakouri A., Milanfar P., Power Trace: An Efficient Method for Extracting the Power Dissipation Profile in an IC Chip from Its Temperature Map, IEEE Transactions on Components and Packaging Technologies, ,Volume 32, Issue 2, June 2009 Page(s):309 - 316
  176. Schuman SG, Koreishi AF, Farsiu S, Izatt JA, Toth CA. Photoreceptor Layer Thinning over Drusen in Spectral Domain Optical Coherence Tomography Imaging of Age-related Macular Degeneration.Ophthalmology, March 2009, 116(3) pp. 488-496.e2,

  177. A. W. Scott, S. Farsiu, L. B. Enyedi, D. K.Wallace, C. A. Toth,"Imagingthe Infant Retina with Handheld Spectral Domain OCT American Journal of Ophthalmology,vol. 147, no.2 pp.364-373, Feb.2009.
  178. G.T. Chong, S. Farsiu, S.F. Freedman, N. Sarin, A.F. Korieshi, J. A. Izatt, C.A. Toth,"Abnormal Foveal Morphology in Ocular Albinism Imaged with Spectral Domain Optical Coherence Tomography", Archives of Ophthalmology, vol. 127, no. 1, pp. 37-44, Jan. 2009.
  179. D. Robinson, S. Farsiu, P. Milanfar Optimal Registration of Aliased Images Using Variable Projection with Applications to Superresolution, The Computer Journal , vol. 52, no.1, pp.31-42, Jan. 2009.

    2008

  180. D. Robinson, S. Farsiu,J.Y. Lo, C.A. Toth, " "Efficient Restoration and Enhancement of Super-resolved X-ray Images ", IEEE International Conference on Image Processing (ICIP), San Diego, CA, pp. 629 - 632 , OCT. 2008.
  181. S. Farsiu, J. A. Izatt, C. A. Toth, " Advances and Emerging Applications of Spectral Domain Optical Coherence Tomography Imaging in Ophthalmology ", "Invited Paper", US Ophthalmic Review, vol. 3, pp. 14-17, 2008.
  182. A. A. Khanifar, S. Farsiu," Spectral-domain OCT in Practice ", "Invited Paper", Retina Today, vol. 3, no.3, pp.49-51, June 2008
  183. H. Takeda, S. Farsiu, and P. Milanfar Deblurring Using Regularized Locally-Adaptive Kernel Regression , IEEE Transactions on Image Processing, vol. 14, no. 4, pp550-563, April 2008.

    184. 2007

  184. Farsiu, S., J. Christofferson, B. Eriksson, P. Milanfar, B. Friedlander, A. Shakouri, R. Nowak,Statistical Detection and Imaging of Objects Hidden in Turbid Media Using Ballistic Photons , Applied Optics, vol. 46, no. 23, pp. 5805-5822, Aug. 2007.

  185. H. Takeda, S. Farsiu, and P. Milanfar,Kernel Regression for Image Processing and Reconstruction, IEEE Transactions on Image Processing,, vol. 16, no. 2, pp. 349-366, Feb. 2007 (2010 IEEE Signal Processing Society Best Paper Award in the Field of Image Proccessing among papers published between 2005-2010).
  186. S.Farsiu, S. J. Chiu, J. A. Izatt, C. A. Toth "Fast Detection and Segmentation of Drusen in Retinal Optical Coherence Tomography Images.", , the Proc. of Photonics West, San Jose, CA, 2008.
  187. D. Robinson, S. Farsiu, J.Y. Lo, P.Milanfar, C.A. Toth, "Efficient Multiframe Registration of Aliased X-Ray Images", Proceedings of the 41th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Nov. 2007, News, BibTex
  188. S. Farsiu and P.Milanfar, "Multi-Scale Statistical Detection and Ballistic Imaging Through Turbid Media", IEEE International Conference on Image Processing (ICIP), San Antonio, TX, Page(s):III - 537-540, Sept. 2007.
  189. X. Wang, A.Shakouri, S. Farsiu and P. Milanfar, "Extraction of power dissipation profile in an IC chip from temperature map", Proc. of 23rd Semiconductor Thermal Measurement, Modeling, and Management Symposium, San Jose, CA, Page(s):51-56, March 2007.
  190. H. Takeda, S. Farsiu, and P. Milanfar, "Higher Order Bilateral Filters and Their Properties", Proceedings of the SPIE Conf. on Computational Imaging, San Jose, 64980S-1:9, January 2007.

    191. 2006

  191. S. Farsiu, M. Elad, and P. Milanfar,Multi-Frame Demosaicing and Super-Resolution of Color Images, IEEE Transactions on Image Processing,, vol. 15, no. 1, pp. 141-159, Jan. 2006. ,

    Color Version of Paper
  192. S. Farsiu, M. Elad, and P. Milanfar Video-to-Video Dynamic Superresolution for Grayscale and Color Sequences , EURASIP Journal of Applied Signal Processing, Jan. 2006.
  193. Regularized Kernel Regression for Image Deblurring, H. Takeda, S. Farsiu, and P. Milanfar, Invited paper, Proceedings of the 40th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Page(s):1914 - 1918, Nov. 2006

  194. H.Takeda, S. Farsiu, P. Milanfar, Robust Kernel Regression for Restoration and Reconstruction of Images from Sparse, Noisy Data , Proc. of the IEEE International Conference on Image Processing (ICIP), Atlanta, GA, Page(s): 1257-1260, October 2006
  195. H. Takeda, S.Farsiu, J. Christou, P. Milanfar, Super-Drizzle: Applications of Adaptive Kernel Regression in Astronomical Imaging", " Advanced Maui Optical and Space Surveillance (AMOS) Technologies Conference, September 2006
  196. S. Farsiu, M. Elad, and P. Milanfar, A Practical Approach to Super-Resolution, Invited paper, Proc. of the SPIE: Visual Communications and Image Processing, San-Jose, Vol. 6077, Page(s): 24-38, January 2006.

    197. 2005

  197. H. Takeda, S. Farsiu, and P. Milanfar, Image Denoising by Adaptive Kernel Regression, Proceedings of the 39th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, Page(s):1660 - 1665, Nov. 2005.

  198. Constrained, Globally Optimal, Multi-Frame Motion Estimation, S. Farsiu, M. Elad, P. Milanfar, Proc. of IEEE Workshop on Statistical Signal Processing, July 2005, Page(s):1396 - 1401, Bordeaux, France.

    199. 2004

  199. S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, Fast and Robust Multi-Frame Super-Resolution ,IEEE Transactions on Image Processing, October 2004, Volume 13, no 10, pp. 1327- 1344.

  200. S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, Advances and Challenges in Super-Resolution ,International Journal of Imaging Systems and Technology , August 2004, Volume 14, no 2, pp. 47-57.

  201. S. Farsiu, D. Robinson, M. Elad, P. Milanfar, Dynamic Demosaicing and Color Super-Resolution of Video Sequences, Proceedings of SPIE Conference on Image Reconstruction from Incomplete Data III, - Volume 5562, August 2004, Denver, CO, Page(s):169-178.
  202. S. Farsiu, M.Elad, P. Milanfar, Multi-Frame Demosaicing and Super-Resolution from Under-Sampled Color Images, IS&T/SPIE Symposium on Electronic Imaging 2004, January 2004 in San Jose, CA. Volume 5299, Page(s): 222-233.

    203. 2003

  203. S. Farsiu, D. Robinson, M. Elad, P. Milanfar, "Fast Robust Super-Resolution", IEEE International Conference on Image Processing (ICIP) Barcelona,September 2003. Volume: 2, Page(s): 291 -294.
  204. S. Farsiu, D. Robinson, M. Elad, P. Milanfar, "Robust Shift and Add Approach to Super-Resolution", International Symposium on Optical Science and Technology, SPIE's 48th Annual Meeting, August 2003, San Diego, CA, Volume 5203, Page(s):121-130.

    205. 2002

  205. R. Rajimehr, S. Farsiu, L. Kouhsari, A. Bidari, C. Lucas, S.Yousefian, F. Bahrami, Prediction of Lupus Nephritis in Patients with Systemic Lupus Erythematosus Using Artificial Neural Networks, Lupus, August 2002, vol. 11, no. 8, pp. 485-492.

Patents:

1. US Patent 7,379,612, "Dynamic Reconstruction of High-Resolution Video from Color-Filtered Low-Resolution Video-to-Video Super-Resolution", issued 2008
2-3. US Patent 7,412,107, and 7,940,282 "System and Method for Robust Multi-Frame Demosaicing and Color Super-Resolution", issued 2008, 2011
4. US Patent 7,477,802, "Robust reconstruction of high resolution grayscale images from a sequence of low resolution frames", issued 2009.
5. US Patent 7,889,950, "Kernel Regression For Image Processing And Reconstruction", issued 2011
6-9. US Patent 8,811,745, and 9,299,155 and 9,589,346 and 10,366,492 "Segmentation and identification of layered structures in images" , issued 2014, 2016, 2017, and 2019, respectively.
10. US Patent 9,940,722 . "Segmentation and identification of closed-contour features in images using graph theory and quasi-polar transform ", issued 2018.
11. US Patent 11,326,870, "Systems and methods for enhanced resolution imaging based on multiple cross-sectional images acquired at different angles", issued 2022
12. US Patent 11,399,930, "Systems and methods for psycho-signal processing", issued 2022

 

Book Chapters:

    1. Robinson D, Chiu S.J., Lo J.Y., Toth C, Izatt JA, Farsiu S, New Applications of Super-Resolution in Medical Imaging, in Super-Resolution Imaging, P. Milanfar (Editor). CRC Press, Pages 383-412, 2010

    2. Toth CA, Farsiu S, Khanifar AA, Chong G, Application of Spectral Domain OCT in AMD, in Optical Coherence Tomography in Age-Related Macular Degeneration, G. Coscas (Editor), (Springer MedizinVerlag Heidelberg, 2009), pp. 15-34:

    3. S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, Simultaneous Demosaicing and Resolution Enhancement From Under-Sampled Image Sequences, in "Single-Sensor Imaging: Methods and Applications for Digital Cameras", R. Lukac (Editor), CRC Press, Pages 503-533, 2008.

    Selected Full-Paper Conference Publications (THI SECTION IS NOT GOING TO BE UPDATED):

    PhD Dissertation:

    A Fast and Robust Framework for Image Fusion and Enhancement , Sina Farsiu, University of California, Santa Cruz, December 2005



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