Job Description

Payroll Title:
Salary Range
Commensurate with Experience
Appointment Type:
Appointment Percent:
Total Openings:
Work Schedule:
Days, 8 hrs/day, M-F

As a federally-funded institution, UC San Diego Health maintains a marijuana and drug free campus. New employees are subject to drug screening.

#113317 Applications Programmer 3

Extended Deadline: Thu 7/7/2022

For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy

UCSD Layoff from Career Appointment: Apply by 12/28/2021 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 01/05/2021. Eligible Special Selection clients should contact their Disability Counselor for assistance.


The UCSD Department of Radiology offers challenging career opportunities cutting-edge research and state-of-the-art services for clinical and translational studies.

The Center for Multimodal Imaging and Genetics (CMIG) is a multi-disciplinary group of scientists, programmers, and support staff that plays a leading role in several national and multinational initiatives involving collection and analysis of imaging, genetic, and behavioral data from healthy controls and patient populations.

CMIG hosts the Data Analysis and Informatics Center (DAIC) of the Adolescent Brain Cognitive Development (ABCD) study, an ongoing, National Institutes of Health (NIH)-funded study to follow ~12,000 children with longitudinal neuroanatomical, functional imaging and behavioral assessments across 21 sites within the US. The major goals of the study are to provide a publicly available data resource to examine the relationships between environmental influences -- including substance use -- and adolescent brain and cognitive development

Applies skills as a seasoned, experienced software professional with a full understanding of industry practices, community standards and relevant policies and procedures to medium-sized projects or portions of large projects with moderate scope and complexity. Resolves a wide range of issues. Demonstrates competency in selecting tools, methods and techniques to obtain results.

Under minimal supervision, implement image processing methods for multimodality medical imaging and neuroimaging data, including structural, diffusion, and functional MRI data. This will include the creation, modification, and containerization of software tools and processing pipelines related to preprocessing T1- and T2-weighted structural images, high-resolution multi-shell dMRI data, and high spatial and temporal resolution fMRI data, automated quality control, manual quality control, intensity nonuniformity correction and cross-site standardization, diffusion model fitting, refinements to cortical surface reconstruction, extracting morphometric and diffusion and intensity-based measures for regions of interest, task-related analysis, resting-state connectivity analysis, extracting functional and summary measures for regions of interest, and data format conversions, including BIDS. Participate as a member of a multi-disciplinary research team in designing, implementing, and documenting data processing tools and pipelines. Support users by effective training and documentation of provided tools.


  • Seven (7) years of related experience, education/training, OR a Bachelor’s degree in related area plus three (3) years of related experience/training

  • Intermediate knowledge of secure software development.

  • Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts.

  • Ability to understand functional needs and how systems can support those needs. Demonstrated ability to develop conversion and system implementation plans.

  • Demonstrated ability to contribute technical narrative to grant proposals.

  • Thorough experience with identification and use of code libraries and open-source forums.

  • Experience with planning for deployment and creation of feedback mechanisms.

  • Proven software repository skills. Demonstrated testing and test planning skills.

  • Thorough experience with common programming tools. Ability to follow software specifications.

  • Effective communication and interpersonal skills. Ability to communicate technical information to technical and non-technical personnel at various levels in the organization.

  • Graduation from college in biomedical engineering, computer science, or a related discipline.

  • Experience working with complex software projects.

  • Extensive experience in programming with MATLAB.

  • Experience in programming with shell scripting.

  • Extensive experience using the Linux operating system.

  • Demonstrated broad problem solving skills. Creativity and the ability to troubleshoot issues as they arise.

  • Experience identifying, troubleshooting, documenting and following technical problems through to completion.

  • Familiarity with statistical analysis methods and strong analytical and problem-solving skills.

  • Strong interpersonal and communication skills. Ability to communicate effectively both orally and in writing.


  • Neuroimaging background.
  • Familiarity with structural, diffusion, and functional MRI research.
  • Familiarity with commonly used neuroimaging data formats; e.g., NIfTI, mgz, analyze.
  • Familiarity with BIDS (Brain Imaging Data Structure).
  • Experience developing software or methods for MRI.
  • Experience with software tools for processing multimodality neuroimaging data.
  • Experience working with DICOM image format data, including transfer, processing, and troubleshooting.
  • Technical understanding of the DICOM (Digital Imaging and Communications in Medicine) Standard digital image format and conversion to other image file formats.
  • Experience in programming with python.
  • Experience applying machine learning techniques.
  • Experience with development and maintenance of open-source or commercial software.
  • Experience writing scripts monitoring and managing jobs in HPC environments, including SGE and Slurm.
  • Experience generating and optimizing containers using Docker/Singularity.
  • Experience with software revision environments, such as GitHub.
  • Experience deploying containers in orchestration environments like Kubernetes and/or Docker Swarm.


  • Employment is subject to a criminal background check.

Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral).

If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable.

UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team!

Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached.

To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community.

UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see:

UC San Diego is a smoke and tobacco free environment. Please visit for more information.

Application Instructions

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