Sina Farsiu

Professor in the Department of Biomedical Engineering

I am the director of the Vision and Image Processing (VIP) Laboratory. Along with my colleagues, we investigate how to improve early diagnostic methods and find new imaging biomarkers of ocular and neurological diseases in adults (e.g. age-related macular degeneration, diabetic retinopathy, Glaucoma, Alzheimer) and children (e.g. retinopathy or prematurity). We also develop automatic artificial intelligence machine learning and deep learning algorithms to detect/segment/quantify anatomical/pathological structures seen on medical images.

On another front, we study efficient signal processing based methods to overcome the theoretical and practical limitations that constrain the achievable resolution of any imaging device. Our approach, which is based on adaptive extraction and robust fusion of relevant information from the expensive and sophisticated as well as simple and cheap sensors, has found wide applications in improving the quality of imaging systems such as ophthalmic SD-OCT, digital X-ray mammography, electronic and optical microscopes, and commercial digital camcorders. We are also interested in pursuing statistical signal processing based projects, including super-resolution, demosaicing, deblurring, denoising, motion estimation, compressive sensing/adaptive sampling, and sensor fusion.

Appointments and Affiliations

  • Professor in the Department of Biomedical Engineering
  • Associate Professor in the Department of Electrical and Computer Engineering
  • Professor of Computer Science
  • Faculty Network Member of the Duke Institute for Brain Sciences

Contact Information

Education

  • B.S. Sharif University of Technology (Iran), 1999
  • M.S. University of Tehran (Iran), 2001
  • Ph.D. University of California - Santa Cruz, 2005
  • University of California - Santa Cruz, 2005
  • University of California - Santa Cruz, 2007

Research Interests

Focused on medical imaging and machine learning to improve the overall health and vision outcome of patients with ocular and neurological diseases (e.g., age-related macular degeneration, diabetic retinopathy, Alzheimer, and ALS) through earlier and personalized therapy.

Courses Taught

  • BME 394: Projects in Biomedical Engineering (GE)
  • BME 493: Projects in Biomedical Engineering (GE)
  • BME 494: Projects in Biomedical Engineering (GE)
  • BME 544: Digital Image Processing (GE, IM)
  • BME 789: Internship in Biomedical Engineering

In the News

Representative Publications

  • Estrada, Rolando, Carlo Tomasi, Scott C. Schmidler, and Sina Farsiu. “Tree Topology Estimation.” Ieee Transactions on Pattern Analysis and Machine Intelligence 37, no. 8 (August 2015): 1688–1701. https://doi.org/10.1109/tpami.2014.2382116.
  • Chiu, Stephanie J., Michael J. Allingham, Priyatham S. Mettu, Scott W. Cousins, Joseph A. Izatt, and Sina Farsiu. “Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema.” Biomed Opt Express 6, no. 4 (April 1, 2015): 1172–94. https://doi.org/10.1364/BOE.6.001172.
  • Polans, James, Ryan P. McNabb, Joseph A. Izatt, and Sina Farsiu. “Compressed wavefront sensing.” Optics Letters 39, no. 5 (March 2014): 1189–92. https://doi.org/10.1364/ol.39.001189.
  • Srinivasan, Pratul P., Stephanie J. Heflin, Joseph A. Izatt, Vadim Y. Arshavsky, and Sina 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.” Biomed Opt Express 5, no. 2 (February 1, 2014): 348–65. https://doi.org/10.1364/BOE.5.000348.
  • Fang, Leyuan, Shutao Li, Ryan P. McNabb, Qing Nie, Anthony N. Kuo, Cynthia A. Toth, Joseph A. Izatt, and Sina Farsiu. “Fast acquisition and reconstruction of optical coherence tomography images via sparse representation.” Ieee Trans Med Imaging 32, no. 11 (November 2013): 2034–49. https://doi.org/10.1109/TMI.2013.2271904.
  • Estrada, Rolando, Carlo Tomasi, Michelle T. Cabrera, David K. Wallace, Sharon F. Freedman, and Sina Farsiu. “Exploratory Dijkstra forest based automatic vessel segmentation: applications in video indirect ophthalmoscopy (VIO).” Biomed Opt Express 3, no. 2 (February 1, 2012): 327–39. https://doi.org/10.1364/BOE.3.000327.
  • Chiu, Stephanie J., Joseph A. Izatt, Rachelle V. O’Connell, Katrina P. Winter, Cynthia A. Toth, and Sina Farsiu. “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images.” Invest Ophthalmol Vis Sci 53, no. 1 (January 5, 2012): 53–61. https://doi.org/10.1167/iovs.11-7640.
  • Estrada, Rolando, Carlo Tomasi, Michelle T. Cabrera, David K. Wallace, Sharon F. Freedman, and Sina Farsiu. “Enhanced video indirect ophthalmoscopy (VIO) via robust mosaicing.” Biomed Opt Express 2, no. 10 (October 1, 2011): 2871–87. https://doi.org/10.1364/BOE.2.002871.
  • Robinson, M Dirk, Cynthia A. Toth, Joseph Y. Lo, and Sina Farsiu. “Efficient fourier-wavelet super-resolution.” Ieee Trans Image Process 19, no. 10 (October 2010): 2669–81. https://doi.org/10.1109/TIP.2010.2050107.
  • Chiu, Stephanie J., Xiao T. Li, Peter Nicholas, Cynthia A. Toth, Joseph A. Izatt, and Sina Farsiu. “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation.” Opt Express 18, no. 18 (August 30, 2010): 19413–28. https://doi.org/10.1364/OE.18.019413.
  • Farsiu, Sina, James Christofferson, Brian Eriksson, Peyman Milanfar, Benjamin Friedlander, Ali Shakouri, and Robert Nowak. “Statistical detection and imaging of objects hidden in turbid media using ballistic photons.” Applied Optics 46, no. 23 (August 2007): 5805–22. https://doi.org/10.1364/ao.46.005805.
  • Farsiu, Sina, Michael Elad, and Peyman Milanfar. “Multiframe demosaicing and super-resolution of color images.” Ieee Transactions on Image Processing : A Publication of the Ieee Signal Processing Society 15, no. 1 (January 2006): 141–59. https://doi.org/10.1109/tip.2005.860336.
  • Farsiu, Sina, M Dirk Robinson, Michael Elad, and Peyman Milanfar. “Fast and robust multiframe super resolution.” Ieee Transactions on Image Processing : A Publication of the Ieee Signal Processing Society 13, no. 10 (October 2004): 1327–44. https://doi.org/10.1109/tip.2004.834669.