Scientific Computing Associate - Software Engineer

3 days left

Howard Hughes Medical Institute
Ashburn, VA
Jul 20, 2021
Jul 27, 2021
Organization Type
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147

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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. Our integrated teams of biologists, computational scientists, and tool-builders pursue a small number of scientific questions with potential for transformative impact. We share our methods, results, and tools with the scientific community. It is a uniquely innovative and collaborative atmosphere that reflects HHMI's reputation for excellence.


The Scientific Computing Associate (SCA) position represents an alternative to the traditional postdoc and provides an ideal environment to establish a career in computational research or software engineering. The position aims at developing qualifications and experience in computational research and professional software engineering in a research environment that enables the candidate to pursue her/his future career in science or industry.

We are looking for a talented and motivated computational scientist to develop algorithms, workflows, and user interfaces for processing large microscopy datasets. The focus of the work will be the reconstruction of terabyte-sized electron microscopy acquisitions produced by the CellMap team at Janelia ( ). This includes development of Java code for image registration, image enhancement, data handling and parallelization on the cluster and in the cloud using established open source libraries like ImgLib2, BigDataViewer, N5, Zarr, Dask, and Spark. Later stages of the project include the development of solutions for user-guided image segmentation based on machine-learning concepts developed within Janelia and the CellMap project which will provide the opportunity for professional development in the domain of machine learning. Therefore, experience with Python and Deep Learning frameworks like PyTorch is a plus.

The developed software will be openly accessible and should be designed to be easy-to-use by developers as well as experimentalists.

In this role the candidate will work closely with experimentalists and microscopists who acquire large-volume light and electron microscopy datasets of cells and tissue as well as with other computational experts. The candidate will be jointly embedded in the CellMap team project and in Scientific Computing departments.

The SCA position is a time-limited appointment for 12 to 24 months, with discretionary renewal for a final 12-month term (maximally 36 months in total).


M.S. or PhD in Computer Science, Bioinformatics, or related field


Experience with writing efficient code with Java or other JVM based languages

Familiarity with Python, other programming languages

Experience with libraries such as Spark and ImgLib2 is a plus

Ideally, you have a record of contributing to open source projects, so we can discuss code. If you do not meet all of the above criteria but you are convinced that you can compensate for this with enthusiasm, creativity, and practical experience, reach out to us and let's talk.

For more information, email Stephan Preibisch and Aubrey Weigel at /

Physical Requirements:

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job's principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word "may," the Essential Duties and Responsibilities described above are "essential functions" of the job, as defined by the Americans with Disabilities Act.

HHMI is an Equal Opportunity Employer

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