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Software Engineer I - Neural Circuits and Behavior - Mindscope

Department: Neural Circuits and Behavior

Software Engineer I Ė Neural Circuits & Behavior


The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Software Engineer I to work as part of a multi-disciplinary team that will carry out a multi-year, large-scale neurophysiological pipeline project to map neural activity across the mouse brain using our Neuropixels Allen Brain Observatory. This individual will play a critical role in rapid development of software for experimental control (including behavior, physiology, and optogenetics), data processing, and data visualization. Because this individual will work closely with the scientific team, we encourage not only software engineers but also scientists looking to transition into software engineering to apply.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Deliver software solutions for neurophysiology and behavioral data collection.
  • Work in close coordination with scientists to write and validate software scripts for running behavioral experiments.
  • Work with scientists to develop, test, and scale computationally-intensive neurophysiology and behavioral processing pipelines.
  • Implement data processing pipelines for large-scale neurophysiological data.
  • Help import and use new neurophysiology and behavioral analysis codebases developed by the external community.
  • Effectively collaborate with scientists on the Brain Observatory team.
  • Meet reasonable but aggressive timelines for engineering solutions.
  • Elicit regular performance feedback from project team to iterate on designs.

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managementís assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • Bachelors degree in engineering, computer science, or equivalent combination of degree and experience (e.g. graduate work in the biological sciences with experience writing/managing software in a lab setting)
  • Experience with scientific programming in Python
  • Working knowledge of version control software, such as Git

Preferred Education and Experience

  • Masterís degree in engineering, computer science, or PhD in neuroscience with an emphasis on neurotechnology, neurophysiology, and/or computation
  • 1 year of work experience in more than one of the following areas of focus: neurotechnology, neurophysiology, psychophysics, systems integration, digital electronics, microprocessors, real-time computing, cluster and cloud computing
  • Experience with systems neuroscience, especially electrophysiology
  • Familiar with agile methods for rapid and flexible software development
  • Experience working in a scientific research environment
  • Experience in two of the following: JavaScript, SQL, C# and Matlab
  • Excellent work ethic displayed as a reliable, self-motivated, enthusiastic team player

Work Environment

  • May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • Occasional lifting to 30 pounds
  • Fine motor movements in fingers/hands to operate computers and lab equipment

Position Type/Expected Hours of Work

  • Occasional evening and weekend hours required
  • This role is currently able to work remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work onsite.


  • Attendance and participation in national and international conferences required

Additional Comments

  • **Please note, this opportunity offers relocation assistance**
  • **Please note, this opportunity offers work visa sponsorship**


It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of ae, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.





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