Job Description

Payroll Title:
Salary Range
Commensurate with Experience
East Campus
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.

#112112 Applications Programmer II

Filing Deadline: Tue 2/8/2022

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 10/12/2021 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 10/21/2021. 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, Resource Center (DAIRC) of the Adolescent Brain Cognitive Development (ABCD) study, an ongoing,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.

Under supervision, implement image processing methods for multimodality medical imaging and neuroimaging data, including structural, diffusion, and functional magnetic resonance imaging (MRI) data. This will include the creation or modification of software tools related to transfer, parsing, manipulation, or conversion of imaging data in DICOM standard format, evaluation of compliance to study-specific image acquisition protocols, and packaging of imaging data in various formats including BIDS. This will also include the creation or modification of software workflows, also known as processing pipelines. Participate as a member of a multidisciplinary research team in designing, implementing, and documenting data processing tools and pipelines. Support users by effective training and documentation of provided tools.

Applies professional programming concepts for small to medium-sized projects or portions of larger projects. Resolves a variety of programming design and implementation issues. Works on programming assignments of moderate scope where analysis of situations or data requires a review of a variety of factors.


  • Six (6) years of related experience, education/training, OR a Bachelor’s degree in related area plus two (2) years of related experience/training.

  • Experience developing software or methods for MRI.

  • Intermediate skills associated with the design, development, modification and deployment of software, including object-oriented programming concepts.

  • Experience with software tools for processing multimodality neuroimaging data.

  • Knowledge of other IT related areas.

  • Demonstrated software repository skills.

  • Experience with common programming tools. Extensive experience in programming with MATLAB. Experience in programming with python. Experience in programming with shell scripting.

  • Experience working with DICOM image format data, including transfer, processing, and troubleshooting.

  • Effective communication and interpersonal skills. Ability to communicate technical information in a clear and concise manner. Ability to communicate effectively both orally and in writing.

  • Strong problem-solving skills. Experience identifying, troubleshooting, documenting and following technical problems through to completion. Strong analytical and problem solving skills. Able to establish and maintain effective working relationships with co-workers and others, interacting and maintaining a strong sense of teamwork and collaboration.Creativity and the ability to troubleshoot issues as they arise.

  • Extensive experience using the Linux operating system.

  • Experience creating cron jobs.

  • Experience generating and optimizing containers using Docker/Singularity.

  • Technical understanding of the DICOM (Digital Imaging and Communications in Medicine) Standard digital image format and conversion to other image file formats.

  • 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).


  • Medical imaging or neuroimaging background.
  • Experience working with medical IT environments (PACS / RIS / EHR).
  • Familiarity with patient privacy regulations, including Health Insurance Portability and Accountability Act (HIPAA) and GDPR.
  • Experience with medical image de-identification procedures.
  • Familiarity with radiology software applications, such as MIM, BrainLab, SyngoVia, AW, Vital, Osirix.
  • Experience creating and editing Standard Operating Procedures (SOPs).
  • 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.
  • Neuroscience and medical imaging experience.


  • Employment is subject to a criminal background check.
  • Must pass a 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).

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.

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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