Scientific Computing Associate – Automating Cognitive Neuroscience Research

Ashburn, VA          ·         Full time

Location: Janelia Research Campus

Time type: Full time

Job requisition ID: R-1540

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.

Scientific Computing Associate – Automating cognitive neuroscience research with machine vision, collaborative robots, game engines, and agent-based modeling

Summary: 

The Scientific Computing Associate II (SCA II) position represents an alternative to traditional scientific roles (e.g. 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 their future career in science or industry.

We are seeking a talented and motivated computational scientist to develop and deploy software to observe, control, analyze, and simulate behavioral neuroscience experiments with freely moving rodents (rats and mice). This requires development and integration of software for machine vision systems, robotic control, and high-performance 3D game engines. In the lab, we use collaborative robots to flexibly reconfigure experimental environments to measure how rodents use intuitive physics to solve novel instances of familiar problems (like fetch). We record behavioral data with high-speed multi-camera systems (each camera generates 2-3GB/s of raw data) and use GPU-accelerated encoding to capture hours-long datasets each day. By integrating real-time machine vision systems with flexible robotic control of behavioral environments, we allow neuroscientists to measure and model animal cognition and intelligence in new and creative ways.

The candidate will work in close collaboration between Scientific Computing Software and the Johnson lab. The candidate will have access to a full spectrum of computational and experimental resources including high performance workstations, CPU/GPU clusters, machine vision cameras, and collaborative robots. The candidate will be embedded in a highly collaborative group of computational scientists, software engineers and cognitive neuroscientists.

The SCA II 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).

Responsibilities:

The candidate will:

• Develop solutions for high-resolution, multi-camera vision systems:
  • Improve and extend a GUI (written in C/C++ with Dear ImGui) to control, stream, annotate, and analyze multi-camera videos.
  • Improve and manage GPU-accelerated video encoding, analysis, and storage pipelines.
  • Train and deploy 3D pose estimation models for animals and objects.
• Develop 3D digital twins of experimental arenas for real-time control and analysis:
  • Use 3D animal, object, and robot pose information to reconstruct experimental data in a 3D game engine (with Unity or Isaac Sim).
  • Integrate machine vision systems with pick-and-place robots to procedurally generate experimental task configurations.
  • Design and deploy a video game to improve human and algorithmic control of experiment flow.
  • Train 3D virtual rodents in the digital twin to solve physics-based reasoning tasks using deep reinforcement learning algorithms.

Qualifications:

Education:

• A degree in computational sciences or equivalent (ideally M.Sc. or Ph.D)
• Experience with C/C++/C# and Python programming languages
• Experience with machine learning and big data
• Experience in solving complex problems independently
• Good communication skills, comfortable working collaboratively in a team environment
• Any experience with machine vision, GPU programming, agent-based modeling, robotics, game development, or reinforcement learning is a plus.

What Janelia Offers You:

• Provide and include you in an environment of computational and experimental enthusiasts
• Skilled scientists and software engineers support the project
• Enable you to work as an independent scientist
• Provide an exciting and inspiring work environment at HHMI Janelia

For specific questions, feel free to reach out to Rob Johnson johnsonr@janelia.hhmi.org & Stephan Preibisch at preibischs@janelia.hhmi.org

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.

Compensation and Benefits

Our employees are compensated from a total rewards perspective in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our Benefits at HHMI site to learn more. 

HHMI is an Equal Opportunity Employer

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