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Scientist I - Electron Microscopic Connectomics

Department: Neural Coding

Scientist I – Electron Microscopic Connectomics - 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 integrate genetic tools with large-scale electron microscopy methods. The scientist will generate enhancer viruses with target expression to sub-classes of neurons and containing molecular reporters that are visible with electron microscopy. The scientist will also participate in the analysis of the resulting EM datasets. 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

  • Develop viral tools to visualize neuronal sub-classes and types in large electron microscopy volumes
  • Collaboratively working with a closely integrated team of scientists and engineers
  • Meeting aggressive project goals with ambitious timelines
  • Coordination with scientific collaborators and resource end-users
  • Publication of scientific results

Additional Functions

  • Analysis of connectivity and morphology data derived from large electron microscopy volumes
  • Software development of analysis tools

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 equivalent combination of degree and experience
  • Demonstrated effectiveness at team-oriented or collaborative work

Preferred Education and Experience

  • 0-5 years postdoctoral, industrial work, and/or research experience
  • Demonstrated ability to rapidly acquire new skills
  • Experience and technical knowledge in design of AAV based gene delivery
  • Analysis of transmission electron microscopy data
  • Experience using Python (common data analysis and visualization packages)
  • Working knowledge of version control software, such as Git
  • Experience with dissemination of open-source resources

Work Environment

  • Laboratory environment - possible exposure to chemical, biological, or other hazardous substances

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
  • This position allows for hybrid remote/on-site work. 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 [note that travel may not always be required to attend]

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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