UC San Diego Shiley Eye Institute UC San Diego Shiley Eye Institute UC San Diego Shiley Eye Institute
by name
Afshari, Natalie A. Brown, Stuart I. Chao, Daniel L. Ferrara, Napoleone Ferreyra, Henry A. Freeman, William R. Goldbaum, Michael H. Granet, David B. Haw, Weldon W. Heichel, Chris W. Kikkawa, Don O. Korn, Bobby S. Lee, Jeffrey E. Lin, Jonathan H. Nguyen, Thao P. Nudleman, Eric Robbins, Shira L. Savino, Peter J. Slight, Rigby Weinreb, Robert N. Welsbie, Derek S. Zhang, Kang
by specialty
Comprehensive Ophthalmology Cornea & Refractive Surgery Glaucoma Neuro-Ophthalmology Ophthalmic Genetics Ophthalmic Pathology Ophthalmic Plastic & Reconstructive Surgery Optometry & Low Vision Pediatric Ophthalmology & Eye Alignment Disorders Refractive Surgery / LASIK Retina & Vitreous Thyroid Eye Clinic
by condition
AMD (Age-related Macular Degeneration) Cataracts Corneal Conditions Cosmetic Surgery Diabetic Retinopathy Eye Movement Disorders Glaucoma Hereditary (Genetic) Disorders Low Vision Neuro-Ophthalmic Conditions Ophthalmic Plastic and Reconstructive Surgery Pediatric Conditions Refractive Errors Retinal Diseases Thyroid Eye Disease

Computational Ophthalmology

The principal goal of our computational ophthalmology group is to make high-performance computing resources easily accessible and provide state-of-the-art, custom software available to vision researchers engaged in cellular, animal, and human vision research studies. In particular, availability of structural imaging instruments such as spectral domain and swept source optical coherence tomography (OCT) and OCT angiography have dramatically increased the size and scale of data collected in ophthalmology, in both research and clinical settings. Improving our understanding of the histopathology of major eye diseases including glaucoma, age-related macular degeneration and diabetic retinopathy requires software tools that aid researchers in managing and processing large-scale image datasets. To this end, we have developed tools to automatically analyze and extract relevant information from OCT images.

The software tools developed by the Computational Ophthalmology group use novel Bayesian, machine learning and deep learning strategies to support computational analyses of both basic science and clinical vision research projects.

Members of our Computational Ophthalmology Group include:

Linda Zangwill, PhD
Akram Belghith, PhD
Christopher Bowd, PhD
Michael Goldbaum, MD
Mark Christopher, PhD

For more information about our Computational Ophthalmology Group contact: viscorecompute@ucsd.edu

Software Tools


San Diego Automated Layer Segmentation Algorithm (SALSA©)


San Diego Automated Layer Segmentation Algorithm (SALSA) is a custom algorithm that takes raw OCT volumes as input and generates retinal layer segmentation. SALSA not only accurately segments retinal layers that are usually provided with instrument software (such as nerve fiber and ganglion cell layers), but also provides measurements that are not routinely provided by instrument software, but are of interest to vision researchers. This includes the choroid, anterior lamina surface, minimum rim width, and beta peripapillary atrophy with intact Bruch’s membrane.

If you use SALSA in your research, please cite these publications.


Citation


The following citations describe the SALSA algorithm in more detail:

Belghith A, Bowd C, Medeiros F, Weinreb R, Zangwill L. Automated segmentation of anterior lamina cribrosa surface: how the lamina cribrosa responds to intraocular pressure change in glaucoma eyes? 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI). 2015; 222–225

Belghith A, Bowd C, Medeiros FA, et al. Does the Location of Bruch’s Membrane Opening Change Over Time? Longitudinal Analysis Using San Diego Automated Layer Segmentation Algorithm (SALSA). Investigative Ophthalmology & Visual Science. 2016;57(2):675-682.

Download SALSA


Here, academic researchers and non-commercial institutions can download a pre-compiled, executable version (Mac and Linux) SALSA to segment the retinal nerve fiber layer from raw OCT volumes.

SALSA is released as is, free for non-commercial use.

To download, please complete the following form and we will email you a link to the software:

K12 Award Program

The overall objective of the NEI Mentored Clinical Scientist Development Program Award at UCSD is to develop outstanding clinician scientists to successfully compete at the national level for NIH grants and emerge as leaders within academic Ophthalmology. Through this institutional career development award, we will mentor clinician scientists toward independent academic appointments in ophthalmology.

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