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.
For more information about our Computational Ophthalmology Group
contact: viscorecompute@ucsd.edu
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.
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.
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:
Information about diversity and inclusion is available through multiple venues. First, there are several websites available that provide information about diversity initiatives across the entire campus (diversity.ucsd.edu) and the (School of Medicine). Many departments have their own websites as well. Virtually all departments at UCSD have identified an Equity, Diversity, and Inclusion (EDI) ambassador, typically a faculty member who spearheads diversity-related initiatives in their areas/specialties and also collaborates with various entities across the medical school.
There are several active affinity organizations for UCSD medical students. These include:
The Association of Native American Medical Students (ANAMS)
The Asian Pacific American Medical Students Association (APAMSA)LGBTQ
Pharmacy and Medical Students (LGBTQ-PhaM)
The Latino Medical Student Association (LMSA)
Medical Students for Justice (MS4J)
The Student National Medical Association (SNMA)
UCSD also offers a curricular pathway called Program in Medical Education – Health Equity (PRIME - HEq), which part of a system-wide effort at the University of California to train physicians better able to meet the needs of the diverse Californian population who are traditionally underserved by the medical system. PRIME-HEq faculty work with students to identify populations or communities at risk for health disparities. Students will then receive exposure, training, and the opportunity to work with the identified group to further their passion in the area and provide knowledge and skills to better equip the students to improve health equity for the group.
