Research Scientist or Postdoctoral Associate-Computer Vision, MouseLight

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


The Howard Hughes Medical Institute's Janelia Research Campus is looking for an outstanding Research Scientist or Postdoctoral Associate interested in applying innovative computational tools to whole-brain imaging datasets imaged with unprecedented resolution and scale. The MouseLight project team is an ongoing collaborative effort involving several experimental research groups at Janelia. The team generates reconstructions of neuronal morphology, tracking individual axonal projections across the entire mouse brain. We seek a candidate interested in automation of neurite identification and reconstruction. Due to the success of the proof-of-concept phase, this project has received additional resources to meet the goals of increased throughput in axonal reconstruction on an aggressive timeline. Individuals interested in developing and/or applying novel image segmentation, machine learning, and optimization algorithms are encouraged to apply. The Janelia Research Campus is a unique, world-class research institute with a major focus on the development of cutting-edge imaging and analysis tools. Candidates interested in this position would be encouraged to work closely with image-processing and machine-learning experts working on related problems at Janelia (e.g., Group Leaders Kristin Branson, Stephan Saalfeld, and Srini Turaga). Individuals interested in pursuing an academic research career or a specialist with experience as a software developer/engineer are encouraged to apply.

Principal Responsibilities:
* Leverage computer vision, pattern recognition and machine learning expertise to innovate and implement state-of-the-art algorithms for detection, segmentation, inference and 3D reconstruction from large scale images.
* Efficiently utilize existing software tools and architectures to meet project goals.
* Work collaboratively with a team of scientists, software engineers, and annotators/proofreaders to implement an effective strategy for next generation high-throughput neuronal morphology identification and reconstruction pipeline.

Preferred Qualifications:
PhD in Computer Science, Applied Math, Physics, Engineering, Neuroscience or a related discipline.
Strong background in image segmentation, and/or image analysis.
Strong understanding of machine vision and machine learning concepts.
Familiarity with high-performance computing and efficient handling of large datasets on modern multi-core or GPU platforms.
Established collaborative programming skills in Java, C/C++, Python or similar languages.
Ability to work and support interdisciplinary work in small groups.
*Ability to develop novel approaches.

Additional Information:
To apply, please upload your CV, cover letter, and include the names and contact information of three references.

HHMI is an Equal Opportunity Employer.

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