Image Processing Software Developer and Production Engineer (JAVA) Consultant

###About HHMI:

Howard Hughes Medical Institute (HHMI) is a science philanthropy whose mission is to advance biomedical research and science education for the benefit of humanity. We empower exceptional scientists and students to pursue fundamental questions about living systems, and work to share scientific discoveries with researchers, students, and science-curious individuals around the world.

Founded in 1953 by aviator and industrialist Howard R. Hughes, HHMI is headquartered in Chevy Chase, Maryland, and employs more than 2,500 people across the U.S. Visit to learn more about working at HHMI.

###About Janelia:

Janelia Research Campus is a pioneering research center in Ashburn, Virginia, where scientists pursue fundamental questions in neuroscience and imaging. The Howard Hughes Medical Institute (HHMI) launched Janelia in 2006, establishing an intellectually distinctive environment for scientists to do creative, collaborative, hands-on work. To learn more about working at Janelia, visit


Within a time-limited (twelve to eighteen month) collaborative project between the Allen Institute for Brain Science and Janelia Research Campus (HHMI) we seek a software engineer/consultant to facilitate the processing of high-throughput serial section transmission electron microscopy data into distortion free volumes for reconstruction of neural connectivity. The software engineer/consultant will be working with engineers at both the Allen Institute for Brain Science and the Howard Hughes Medical Institute (Janelia Research Campus) in Ashburn, VA. The position is based in Ashburn, VA, and some travel is expected.


  • Design and production of end-to-end data flow pipeline for large scale image registration
  • Expand existing Java and Matlab libraries
  • Wrapping the pipeline as a service
  • Documenting and administering individual components
  • Training other production engineers and scientists to use and expand the pipeline

###Principal Responsibilities:

  • Will work closely with scientists & software engineers to oversee infrastructure for manipulating peta-scale electron microscopy data
  • Will work on automation of existing image data registration, processing and curation
  • Diagnose and troubleshoot, both independently and collaboratively
  • Evaluate & learn new software tools, practices & algorithms

###Preferred Qualifications:

  • Education: B.S. or M.S. in Computer Science or related field (or equivalent education and experience)
  • Strong familiarity with Linux
  • Proficient in Java
  • Preferred: Experience with utilizing SQL and/or NoSQL data stores (e.g. MongoDB, PostgreSQL)
  • Preferred: Experience with image processing (ImageJ, Fiji or other)
  • Preferred: Experience with Matlab
  • Familiar with RESTful web services
  • Experience using Spark on an HPC cluster
  • Comfortable working with new programming languages and tools when necessary

HHMI is an Equal Opportunity Employer.


I would love to develop image processing suites using ImageJ, Matlab and Java. Neural imagery would be particularly interesting since I’ve been working in AI for some time now. I’m currently developing diagnostic software for diseases of the ear as imaged via Otoscope. I enjoy rapid prototyping and algorithm discovery. I have a BS is physics and have been doing machine vision most of my career. I’m currently interested in machine learning as applied to imagery, and your job search in the ImageJ Forum is very interesting to me. Please contact me at so I can share my CV with you. I will want to work mostly online with travel for meetings with other teammates.

Yours Truly
Ron DeSpain