I am the director of the Vision and Image Processing (VIP) Laboratory and a professor of Biomedical Engineering and Ophthalmology with secondary appointments at the Departments of Electrical and Computer Engineering and Computer Science, and the Director of Graduate Studies for the Master’s Program in Biomedical Engineering at Duke University. I have served as the Senior Area Editor of IEEE Transactions on Image Processing, Deputy Editor of the Biomedical Optics Express, and the Associate Editor of SIAM Journal on Imaging Sciences. I am a Fellow of IEEE, OSA, SPIE, ARVO, and AIMBE.
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 deep learning, 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.
1. Medical Image Analysis ML-based Software Development:
A major focus of our lab is the development of fully automated software, using deep learning and other advanced machine learning technologies, 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 and machine learning ideas, mainly super-resolution, demosaicing/deblurring/denoising, motion estimation, compressive sensing/adaptive sampling, segmentation, and sensor fusion.
3. Advanced Ophthalmic Imaging Hardware Development:
In collaboration with our colleagues at the department of biomedical engineering, especially the Laboratory for Biophotonics, we develop the next generation ophthalmic imaging systems, including advanced handheld OCT and adaptive optics ocular imaging systems.
June 2023: Ph.D. student Ziyun Yang has made the software for his medical CVPR image segmentation method paper available online.
May 2023: Dr. Jessica Loo received the 2022-23 BME Ph.D. Dissertation Award.
August 2021: Ph.D. student Ziyun Yang has made the software for his exciting BiconNet semantic segmentation method in his Pattern Recognition paper available online.
July 2020: Congrats to our recently graduated Somayyeh Soltanian-Zadeh for receiving the $100,000 Hartwell Postdoctoral Fellowship.
April 2019: Congrats to our incoming PhD student Kevin Choy for receiving the NSF GRPF Fellowship.
April 2019: PhD student Somayyeh Soltanian Zadeh has made the software and dataset for her new PNAS paper open source and freely available online.
April 2019: Congrats to my former undergraduate research assistants/Pratt Fellows, Arjun Desai and Eli Cole, for receiving the NSF GRPF Fellowship; we wish them success in their PhD studies at Stanford and Caltech, respectively.
November 2018: News release about Arjun Desai's paper on our open source automated software for detection of infants' gestational age through smartphone lens imaging.
November 2018: Call for papers in Neurophotonics special issue on "Advanced Retinal Imaging: Instruments, Methods, and Applications" which I'll be guest co-editing.
August 2018: News release about our paper on handheld adaptive optics scanning laser ophthalmoscope (HAOSLO). Also, we have made the Zemax optical design, Solidworks mechanical design, and LabView software, controlling the HAOSLO hardware open source and freely available online.
July 2018: Congrats to PhD Student Jessica Loo for receiving the John Chambers Scholar Award.
June 2018: Congrats to PhD Student Jessica Loo for receiving the First prize for outstanding research at the annual Duke Ophthalmology Trainee day Scientific Symposium.
April 2018: Congrats to the incoming PhD student to our laboratory, Ali Hassan for receiving the NSF GRPF Fellowship.
March 2018: Congrats to PhD student Jessica Loo for receiving the 2nd Place poster award for her work on deep learning based OCT image analysis at theFitzpatrick Institute for Photonics Annual Meeting.
Jan. 2018: Congrats to PhD student David Cunefare for receiving the Retina Research Foundation/ Joseph M. and Eula C. Lawrence Travel Grant to present his exciting research on deep learning based adaptive optics image analysis at the ARVO 2018 Annual Meeting in Honolulu, Hawaii.
November 2017: You want to know if there is room for improving the accuracy of layer segmentation algorithms? Theo Dubose’s exciting new paper shows the theoretical lower bounds on the accuracy of retinal layer segmentation methods. His paper also accurately derives retinal layer specific statistical models of signal and noise in OCT imaging. PREPRINT
July 2017: David Cunefare's Open source software for automatic detection of cone photoreceptors in adaptive optics ophthalmoscopy using convolutional neural networks is now freely available online (click here for the code and dataset )
May 2017: Congrats and best wishes to Dr. Rolando Estrada for being appointed as a tenure-track Assistant Professor of Computer Science at the Georgia State University. Congrats to our ECE Pratt Fellow Eli Cole for graduating with distinction and winning the 2017 Charles Ernest Seager Memorial Award recognizing the most outstanding undergraduate research project in the ECE Department, and wishing him the best in the EE PhD program at Caltech. Congrats to our BME Pratt Fellow Leon Cai for graduating with distinction and winning the 2017 Clark Award in the BME Department, and wishing him the best success in the MD/PhD program at Vanderbilt University.
Jan. 2017: Excited about our new paper on predicting the response to anti-VEGF treatment!.
Jan. 2017: Congrats to our outstanding undergrad Pratt Fellow researcher, Eli Cole, for receiving the 1st place award in the Fall 2016 Duke ECE Independent Study Poster Session.
Jan. 2017: Excited and honored to receive the " the Association for Research in Vision and Ophthalmology (ARVO) 2017 Pfizer Ophthalmics Carl Camras Translational Research Award".
Nov. 2016: Jose Lezama has made publically available source code for his work on "Registration of wide field-of-view retinal optical coherence tomography volumes"
Sept. 2016: Leyuan Fang has made publically available software for his work on "Segmentation based sparse reconstruction of retinal optical coherence tomography volumes"
June 2016: Congrats to PhD student Somayyeh Soltanian-Zadeh for being awarded Pre-doctoral NIH Fellowship in the Medical Imaging Training Program (MITP).
June 2015: Congrats to PhD Student David Cunefare Jr. for receiving the $94,000 John T. Chambers Scholar award.
June 2015: Rolando Estrada has made publically available two datasets of annotated wide field-of-view color retinal images utilized in his recent IEEE PAMI paper on tree topology estimation and IEEE TMI paper on artery vein classification.
April 2015: Congrats to my former undergraduate research assistant/Pratt Fellow, Pratul Srinivasan, for receiving the NSF GRPF Fellowship; we wish him success in his PhD studies at UC Berkeley.
March 2015: Stephanie Chiu's solution to one of the most challenging automated OCT segmentation problems (layers and cysts in low-quality diabetic macular edema images) is published and dataset of annotated images is now freely available online.
March 2015: Hossein Rabbani has made the full dataset of annotated fluorescein angiography images from diabetic macular edema patients utilized in his paper featured on the cover of IOVS freely available online.
February 2015: We made large datasets of annotated images from multiple studies on diabetic macular edema (SD-OCT ) freely available online.
December 2014: Congratulations to our outstanding High School research intern Elizabeth Chiu for being admitted to Duke University.
December 2014: Rolando Estrada's fundamental work on graph-theory is now accepted for publication in IEEE T-PAMI. This paper provides a practical solution for estimating the 3-D topology of tree-like structures (e.g. vessels and plant roots) from a single 2D image.
September 2014: The second first authored journal paper of our recently graduated outstanding undergrad Pratt Fellow, Pratul Srinivasan, is now published .
August 2014: New patent no. 8,811,745 issued: Segmentation and identification of layered structures in images.”
May 2014: Congratulations to Dr. Stephanie Chiu for officially receiving her well deserved PhD degree after co-authoring over 20 journal papers during her tenure at VIP lab.
May 2014: Congratulations to our outstanding Pratt Fellow Pratul Srinivasan for being admitted to all top ranking ECE PhD programs in USA.
May 2014: Congratulations to our outstanding High School research intern Alec V. Arshavsky for being admitted to Stanford University.
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!
August 2013: Congrats to our new PhD student David Cunefare for being awarded Pre-doctoral NIH Fellowship in the Medical Imaging Training Program (MITP).
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: 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: 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.
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.
Emails without appropriate codes may directly go to my SPAM box!
2022-23 PhD Student Applicants: I expect to recruit BME PhD students with interests in AI-based medical image analysis (software)or adaptive optics SLO or OCT imaging (hardware).
US residents with a minimum 3.6 GPA from a top US school may contact me directly via email (please type the code "USGS-2022" in the subject of your email).
International students: I receive hundreds of inquiries from students interested in joining my group, thus, I maybe unable to answer each person individually. You are certainly welcome to contact me 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 (please type the code "i-USGS-2022" in the subject of your email).
Current Duke Undergraduate/Graduate Students:Current Duke students (BME, EE, CE, or CS) interested in AI-based medical imaging/image processing-related projects can contact me directly via email (please type the code "i-MSGS-2022" if you are an MS and "i-DUS-2022" 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-2022" in the subject of your email).
Postdoctoral Research Associate #1: The minimum requirement is multiple first-authored high-quality image-processing journal publications (e.g., papers in IEEE TIP, CVPR/ICCV, and IEEE PAMI). I am mainly interested in deep learning-based image analysis expertise. You must have a GoogleScholar page before applying for this position.
Postdoctoral Research Associate #2: Applicants with ocular adaptive optics design expertise are welcome to apply for a postdoc position jointly with Prof. Joseph A. Izatt. Please type the code "PD-2022" in the subject of your email.