Scalable modeling and visualization of central nervous system sub-structures from terabytes of neuro-imaging data to study the pathology of Multiple Sclerosis
Roland Henry, Professor
UC San Francisco
Closed. This professor is continuing with Spring 2024 apprentices on this project; no new apprentices needed for Fall 2024.
UCSF’s Department of Neurology has some of the largest clinical neuroimaging datasets in the world. As the director of imaging for the multiple sclerosis group, Dr. Roland Henry’s laboratory is in charge of making sense of this data and applying next generation analytical techniques to translate this raw data into actionable clinical results.
The laboratory is recruiting talented computational and data scientists to help build scalable distributed processing tools to efficiently process, analyze, and visualize data from a unique large cohort of patients to pilot precision medicine with MRI quantitative metrics.
This group is trying to build a big data platform for scalable analysis of terabyte of neuroimaging data. To do this, we need talented folks who can understand how to build clinically useful models of the central nervous systems that can be efficiently stored at scale.
We also aim to develop novel visualizations and engineer multiple data layers so the data is accessible to be analyzed by folks of various technical skill levels. For example, an early undergraduate project was build a model of the neural pathways between the regions of the brain involved in visual processing and building several network models of these pathways. To make this more accessible, a database of network models and visualization of these pathways needed to be engineered so neurologists could analyze how these pathways were affected by disease.
Role: An undergraduate would contribute to the following initiatives
(a) extending the suite of tools to process and understand 3D imaging data, (b) assessing the clinical value of quantitative neuroimaging biomarkers, (c) accelerating and extending the computational advanced clinical analytics on neuroimaging data, (d) building streaming platforms to visualize 3D imaging data annotated with clinical biomarkers, (e) building mobile and other platforms to facilitate human in the loop quality assurance and annotation, and (f) extending our data infrastructure to be able to efficiently store and disseminate clinical results
Qualifications: We are looking for talented software engineers who have an interest in building scalable applications. This involves UI/UX designers, software engineers, mobile application developers, and especially people with an interested in distributed systems.
There are no hard and fast qualifications for this position but ideally the individual in question has a passion for building and maintaining complex software processing tools and end-user applications. As medicine becomes increasingly data driven, UCSF needs talented programmers who can enable clinicians to be able to provide next-generation care.
We have projects to stream analytical results for neuro-surgical applications, segment anatomical structures to build real-time modeling of human systems, compute chemical biomarkers to monitor the progress of disorders, and many more projects all which have bottlenecks due to a lack of programming talent. We hope you’ll be able to help us monitor, diagnose, and hopefully cure neurodegenerative disorders with programming!
We spend the first semester on a "low hanging fruit project" and training. This semester will give undergraduates a broad exposure to projects in the center. As such, we usually ask undergraduates to consider a year-long commitment.
Day-to-day supervisor for this project: Amit Vijay Akula, Staff Researcher
Hours: 9-11 hrs
Off-Campus Research Site: * As this is a data-intensive project, much of the work can be done remotely at any place with a sufficiently fast internet connection * The day-to-day mentors for the project work at the Sandler Neuroscience Center at UCSF Mission Bay. * For the first semester, we do ask that a half-day (or sometimes a full-day) is spent in person at UCSF Mission Bay
Biological & Health Sciences Education, Cognition & Psychology Engineering, Design & Technologies