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Scientist I - Virtual Observatory of the Cortex

Department: Neural Coding

Scientist I – Community Manager - Virtual Observatory of the Cortex - Neural Coding


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 mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling, and theory.

The Neural Coding department examines the relationship between neural circuits and neural dynamics by combining in vivo functional imaging with ex vivo state of the art electron microscopy (EM). We provide resources to the neuroscience community to accelerate community progress towards these aims (

We are seeking a scientist to work as a part of an integrated team of scientists and engineers to disseminate data and knowledge from these datasets to the larger scientific community through the Virtual Observatory of the Cortex project. The scientist will interface with the larger scientific community, gathering requests on proofreading, annotation, and analysis projects they are interested in. The scientist will work to understand the scientific goals behind the requests and develop plans for proofreading, annotation, and analysis that help meet those goals. The scientist will synthesize and present these plans to the scientific steering committee, and back to the scientific community in written and spoken form. The scientist will contribute to state-of-the-art open-source analysis tools and workflows for large-scale electron microscopy data, along with tutorials on how to use those tools to help the broader scientific community access and analyze the data. We prioritize applicants with demonstrated creative problem-solving skills and the ability to work in collaborative environments with aggressive timelines.

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

  • Communicate with a broad scientific audience to understand their scientific interests and translate them into actionable proofreading and annotation plans
  • Develop analysis methods and software tools to facilitate the analysis of connectivity and morphology data derived from large electron microscopy volumes
  • Write and deliver reports that summarize scientific progress with the dataset
  • Coordination with scientific collaborators and resource end-users
  • Publication of scientific results

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

Required Education and Experience

  • PhD degree in biology, physics, cell science, neuroscience, engineering, or other discipline related to essential functions; or an equivalent combination of degree and experience
  • Demonstrated ability to develop a complex quantitative analysis of neural data
  • Python and common scientific data analysis and visualization packages

Preferred Education and Experience

  • 0-2 years of postdoctoral or industrial experience
  • Demonstrated effectiveness at team-oriented or collaborative work
  • Working knowledge of version control software, such as Git
  • Experience with the dissemination of open-source resources

Physical Demands

  • Occasional lifting up 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
  • Will enter laboratory environment, including potential exposure to lasers, biohazards
  • This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.


  • Attendance and participation in national and international conferences required

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance.

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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