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Scientist I - Neural Coding

Department: Neural Coding

Scientist I – 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 develop an open-source hardware/software resource for or automated serial section ultramicrotomy with broad applications to high throughput transmission and scanning EM. 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

  • Working with a closely integrated team of scientists and engineers
  • Serial-section ultramicrotomy of brain tissue for 3D EM reconstructions
  • Creative problem solving for automation of serial section collection
  • Meeting aggressive goals with ambitious timelines
  • Coordination with scientific collaborators and resource end-users
  • Management of contractor relationships
  • Collaborative system testing and integration of both hardware and software. 
  • Publication of scientific results
  • Analysis of data derived from large electron microscopy volumes
  • Open-source resource platform development
  • Software development on motion control, machine vision
  • Design and deployment of hardware solutions

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 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

  • Demonstrated ability to rapidly acquire new skills
  • 0-6 years postdoctoral or industrial experience
  • Ultramicrotomy and serial section transmission electron microscopy
  • Testing/development of scientific hardware
  • Efficient using C++ (Qt, opengl) and Python (common data analysis and visualization packages)
  • Development on motion control systems
  • Working knowledge of version control software, such as Git
  • Experience with closed-loop object tracking
  • Experience with CAD/3D modelling software such as Fusion 360
  • Management of contractor relationships
  • Experience with dissemination of open-source resources

Work Environment

  • Will 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 other office equipment; repetitive motion with lab equipment
  • Push/pull up to 30lbs
  • 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. 


  • Attendance and participation in national and international conferences required. (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 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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