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Scientist II - Neural Coding

Department: Neural Coding

Scientist II –  Neural Coding - Allen Institute for Brain Sciences


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.

We are seeking a neuroscientist to lead the effort in image processing and analysis of large-scale Electron Microscopy (EM) datasets. The scientist will be responsible for overseeing EM image processing and will participate in the analysis of large-scale datasets. Examples of work related to this position can be found on:


The scientist will be an essential member of the EM connectomics project studying cell types across multiple modalities and their relationship with brain function.

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

  • Collaborate with others to further scale the image processing of a high throughput electron microscopy pipeline beyond petascale datasets.
  • Overseeing EM data 2D stitching and 3D alignment
  • Analyze EM data in the context of neuronal cell types
  • Work closely with a team of anatomists, physiologists, theoreticians, and modelers to analyze and interpret the relationship between structure and modalities of cells such as molecular and physiology properties
  • 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 management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • PhD in Neuroscience, Computational Neuroscience, Computer Science, Applied Math, Material Sciences or related field; or equivalent combination of degree and experience
  • Minimum of 3 years experience with relevant computer programing

Preferred Education and Experience

  • Experience with Python
  • Experience in image processing
  • Machine learning experience
  • Excellent verbal and written communication skills

Work Environment

  • Laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • Occasional lifting up to 30 pounds
  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment
  • Stooping, bending, crouching
  • Reaching, or climbing ladders

Position Type/Expected Hours of Work

  • Occasional evening and weekend hours required  
  • This role is currently working onsite and remotely when possible, due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees.


  • Occasional travel to partner sites for compliance oversight required
  • Attendance and participation in national and international conferences required

Additional Eligibility Qualifications

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

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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