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Scientist I - Machine Learning in Circuit Tracing

Department: Neural Dynamics - Molecular Anatomy

Scientist I - Machine Learning in Circuit Tracing - Neural Dynamics

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 Allen Institute has been a leader in the field of neuroscience for over 17 years; in 2021 we are launching a new research division to understand how dynamic neuronal signals at the level of the entire brain implement fundamental computations and drive flexible behaviors. Using a team science approach, we strive to uncover the neural basis of behavior through technological innovation, cutting-edge experiments, modeling, and theory.

As part of this initiative, we plan to generate high-throughput images of the complete arbors of individual neurons. Both the size and the complexity of these datasets require an automated approach to the reconstruction of neuronal arbors. We are seeking to fill a position at the level of Scientist to work with the Instituteís quantitative and experimental scientists on high-priority problems in neuronal reconstruction and analysis that include (i) topology-preserving approaches to neuronal segmentation, (ii) deep learning-based analysis of morpho-molecular datasets, and (iii) high performance computing.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. Progress in science benefits from multiple perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Develop novel algorithms to improve the quality of neuron reconstruction in whole-brain images
  • Analyze the quality of resulting reconstructions
  • Develop novel methods to improve the overall throughput of a human-in-the-loop pipeline
  • Participate in a highly interactive and multidisciplinary environment
  • Publish/present findings in peer-reviewed journals/scientific conferences

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

  • PhD degree in computer science, neuroscience, physics, mathematics, applied mathematics, engineering, or related field, or equivalent combination of degree and experience
  • Demonstrated proficiency in scientific computing

Preferred Education and Experience

  • 0-4 years postdoctoral experience
  • Experience in image segmentation with neural networks
  • Experience with modern machine learning paradigms such as reinforcement learning and supervised learning
  • Experience in computational topology
  • Experience in high-performance computing
  • Ability to work in a collaborative environment
  • Proven independent thinking
  • Experience in computational neuroscience
  • Strong publication record

Work Environment

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

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and lab equipment

Position Type/Expected Hours of 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

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 age, 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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