Sina Farsiu, PhD

Sina Farsiu Farsio Super-Resolution superresolution optical coherence tomography oct sd-oct segmentation retina

Assistant Professor
Department of Ophthalmology
Department of Biomedical Engineering
Department of Electrical & Computer Engineering
Department of Computer Science

Duke University

Associate Editor: IEEE Transactions on Image Processing

Mailing AddressBOX 3802, DUMC, Durham, NC, 27710
OfficeRoom 5014, AERI Building
Phone :919-684-6642
Fax:919-684-8983

Email: sina DOT farsiu AT duke DOT edu

SEE OUR PUBLICATION PAGE FOR:

Automated Segmentation of Ocular Images

CHIU SEGMENTATION SDOCTcornea sina farsiu

drusen geographic atrophy chiu farsiu sina segmentation automatic

mouse retina rhoko Rho(−/−) Pratul P. Srinivasan farsiu sina segmentation automatic

Retinal pigment epithelium rpe cell sina farsiu automatic  segmentation confocal microscopy adaptive optics

  sina farsiu automatic  segmentation retina retinal vasculature vessel video indirect ophthalmoscopy Exploratory Dijkstra forest

  sina farsiu automatic  segmentation cell  cone rod SLO scanning laser ophthalmoscope  adaptive optics

Photonic Imaging:

Sina Farsiu Ballistic Photon

Ballistic Photon adaptive sampling compressive sensing

Speckle Variance Doppler Swept Source OCT Mosaic Capillary Registration

Adult/Pediatric Ophthalmic Research and Image Analysis

 Farsiu AMD age related macular degeneration ophthalmology retina sdoct control drusen geographi atrophy

Maldonado Farsiu pediatric ophthalmology retina sdoct prematurew

Fast Wavefront Sensors

Compressed sensing wavefront sensor adaptive optics retina cone rod cones rods

Optimized Handheld SLO

Scanning laser ophthalmoscope spectralis heidelberg sina farsiu

 

Vision and Image Processing (VIP) Laboratory

VIP LAB DUKE UNIVERSITY SINA FARSIU 2013
VIP LAB DUKE UNIVERSITY SINA FARSIU 2012
VIP LAB DUKE UNIVERSITY SINA FARSIU 2011

VIP Lab members "occupying" a sushi restaurant!

SEE OUR PUBLICATION PAGE FOR:

Image Reconstruction

Low-Quality Input Images on Left, High-Quality Reconstructed Images on Right

Interpolation Denoising sparsity compressive sensing AMD drusen geographic atrophy Sina Farsiu SD-OCT

Denoising sparsity compressive sensing Sina Farsiu SDOCT

mosaicing vio video indirect ophthalmoscopy vessel segmentation registration Sina Farsiu

 video superresolution super resolution super-resolution kalman filter registration Sina Farsiu

  wavelet deblurring breast cancer digital tomosynthesis superresolution super resolution super-resolution xray  registration Sina Farsiu

   multiframe demosaicing demosaicking color superresolution super resolution super-resolution Sina Farsiu

  kernel regression interpolation denoising super-resolution  Sina Farsiu

   sdoct oct spectral domain optical coherence tomography vessel registration superresolution medical super-resolution  Sina Farsiu

Multimodal Photonics Imaging    sdoct oct spectral domain optical coherence tomography vessel registration  scanning laser ophthalmoscope SLO handheld  Sina Farsiu

Surgical Microscope Integrated OCT

Surgical SDOCT

Optimized Handheld SLO

Generalized Pseudo-Polar Fourier Grids

Generalized Pseudo-Polar Fourier registration Sina Farsiu

 

About

I am the director of the Vision and Image Processing (VIP) Laboratory at Duke University. At VIP lab, our long-term goal is to improve the overall health and vision outcomes of at-risk patients with ocular and neurological diseases through earlier and better-directed therapy. To achieve this goal, we take advantage of recent advances in image processing and optics as an integrated technology to capture ocular images with higher resolution and better motion stability compared to the state-of-the-art imaging systems. Once these high-quality images are captured, we provide objective tools to quantitatively measure novel imaging biomarkers of the onset and progression of ophthalmic and neurological diseases.

VIP Lab’s Research Focus

1.      Image Analysis Software Development for Ophthalmology and Vision Sciences:

We collaborate with our clinical colleagues, including Duke Advanced Research in SDOCT Imaging Laboratory. A major focus of our lab is development of fully automated software to objectively detect and evaluate the biomarkers for onset and progression of ocular and neurological diseases in adults (e.g. diabetic retinopathy, age-related macular degeneration (AMD), Glaucoma, and Alzheimer's disease) and children (e.g. retinopathy or prematurity (ROP)). We also develop automatic segmentation algorithms to detect/segment/quantify ocular anatomical/pathological structures seen on ophthalmic imaging systems such as Optical Coherence Tomography (OCT) and adaptive optics scanning laser ophthalmoscopy (AO-SLO).

2.      Image Processing Theory and Application:

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, video indirect ophthalmoscopy, digital X-ray mammography, electronic and optical microscopes, and commercial digital camcorders. When I am not busy developing a mathematical model of the procrastination theory, I play with some statistical signal processing ideas, mainly super-resolution, demosaicing/deblurring/denoising, motion estimation, compressive sensing/adaptive sampling, and sensor fusion.

3.    Advanced Ophthalmic Imaging Hardware Development:

In collaboration with our colleagues at the department of biomedical engineering, especially the Laboratory for Biophotonicswe develop the next generation ophthalmic imaging systems, including advanced handheld OCT and adaptive optics ocular imaging systems.

News

February 2014:  James Polans put the fast compressed sensing based wavefront measurement software freely available online.

January 2014:  Congrats to our high school research intern, Alec V. Arshavsky for winning the North Carolina International Science Challenge; he will represent USA in the next round of competition in Beijing, China. Also, congrats to Alec for being selected as a finalist in the Intel Science Talent Search (Intel STS).

December 2013:  Yeay! Our team of collaborators from different disciplines received Bass Connections funding for our proposed project "Art, Vision and the Brain: An Exploration of Color and Brightness". It will be fun!

September 2013:  We have made the world's largest online atlas of annotated SD-OCT images from intermediate AMD and control subjects used in our recent paper available online.

August 2013:  Congrats to our new PhD student David Cunefare for being awarded Pre-doctoral NIH Fellowship in the Medical Imaging Training Program (MITP).

July. 2013: Leyuan Fang has put complete study dataset and software for his recent IEEE TMI paper "Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation", freely available online.

June 2013:  Yeay! Our team of collaborators from different disciplines received DIBS pilot funding to study ophthalmic imaging biomarkers in early Alzheimer’s disease!

May 2013:  Congrats to our undergrad Pratt Fellow Dazhong (Chime) Xuan for receiving the Theo C. Pilkington Memorial Award in recognition of his outstanding perseverance and accomplishment in the study of biomedical engineering.

May 2013:  Complete study dataset including automated and manual markings for our AO-SLO cone photoreceptor automatic segmentation paper is available online.

May 2013:  Congrats to Stephanie Chiu for advancing to PhD candidacy after co-authoring 18 (published/submitted) journal papers

July 2012:  Yeay! We got NIH R01 funding to develop software for automated classification of diabetic macular edema.

June 2012: PhD Student Stephanie Chiu received First prize for outstanding research at the annual Duke Ophthalmology Trainee day Scientific Symposium for the record "third times" in a row.

April. 2012: Leyuan Fang has put complete study dataset and software for his BOE paper "Sparsity Based Denoising of Spectral Domain Optical Coherence Tomography Images ", freely available online.

April. 2012: Yeay! We received NCBC funding to build a novel Ultrahigh-Resolution Adaptive Optics Optical Coherence Tomography/Scanning Laser Ophthalmoscopy System systems at DUEC.

April 2012: Stephanie Chiu has put the  complete study dataset including our automated and manual markings for her May 2012 BOE paper "Automatic segmentation of closed-contour features in ophthalmic images using graph theory and dynamic programming" online.

April 2012: Francesco LaRocca as put the  complete study dataset including our automated and manual markings for his June 2011 BOE paper "Robust Automatic Segmentation of Corneal Layer Boundaries in SDOCT Images using Graph Theory and Dynamic Programming" online.

Feb. 2012: Rolando Estrada has put complete study software (MATLAB Code) and dataset including our automated and manual markings for his BOE paper Exploratory Dijkstra forest based automatic vessel segmentation: applications in video indirect ophthalmoscopy (VIO)", freely available online.

January 2012: Stephanie Chiu has put the  complete study dataset including our automated and manual markings for her Jan. 2012 IOVS paper "Validated Automatic Segmentation of AMD Pathology including Drusen and Geographic Atrophy in SDOCT Images" online.

January 2012:  Yeay! We got NIH funding to build the next generation of handheld SD-OCT systems.

June 2011: PhD Student Stephanie Chiu received First prize for outstanding research at the annual Duke Ophthalmology Trainee day Scientific Symposium.

Feb. 2011: PhD Student Stephanie Chiu received the National Eye Institute travel award for her ARVO abstract.

Feb. 2011: 2010 IEEE Signal Processing Society -Best Paper Award  (Kernel Regression for Image Processing and Reconstruction, in IEEE Transactions on Image Processing). 

Nov. 2010: PhD Student Stephanie Chiu received $80,000 Chambers Fellowship

Oct. 2010: PhD Student Stephanie Chiu  received 3rd prize for best poster at the Annual Meeting of the Fitzpatrick Institute for Photonics

June 2010: PhD Student Stephanie Chiu received First prize for outstanding research at the annual Duke Ophthalmology Trainee day Scientific Symposium.

Apr. 2010: PhD Student Rolando Estrada  received AFER/Retina Research Foundation Student Travel Award for his ARVO abstract.


AVAILABLE POSITIONS

Emails without appropriate codes may directly go to my SPAM box!

Postdoctoral Research Associate: The minimum requirement is three first-authored high-quality image-processing journal publications (e.g. papers in IEEE TIP or IEEE PAMI) in the past three years (UPDATE: Positions Filled. You may send me CVs for future possible openings, please type the code "PD-2014" in the subject of your email).

2014 PhD Student Applicants:  I occasionally recruit one BME, EE, CE, or CS majors applying to Duke PhD programs in BME or ECE and interested in image processing/photonics/ophthalmology related projects per year. l will only recruit students with exceptionally high achievements during undergraduate studies as evident by GPA from highly selective undergrad schools and/or high-impact peer-reviewed publications.

US residents with minimum 3.7GPA from a top US school may contact me directly via email (please type the code "USGS-2014" in the subject of your email).

International students: I receive hundreds of inquiries from students interested in joining my group, thus I am unable to answer each person individually. You may contact me only if you have "already" submitted your application to Duke. In that case, please let me know that you are interested in working with me and I will look at your full application at Duke's website.

Exception is for the international students with financial aid from their own country. I will review their CV in PDF format before applying to Duke (please type the code "i-USGS-2014" in the subject of your email).

Current Duke Undergraduate/Graduate Students: Current Duke students (BME, EE, CE, or CS) interested in image processing/ophthalmology related projects can contact me directly via email (please type the code "i-MSGS-2014" if you are an MS and "i-DUS-2014" if you are an undergrad in the subject of your email).


Duke's 3rd Year Medical Students: Medical students interested in participating in ophthalmic imaging related projects may contact me directly. Please send me an email (please type the code "DMS-2014" in the subject of your email).