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Scientist I – AIx2

Department: Brain AIx2 Management
Location: Seattle

Scientist I – AIx2 

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.  

We are seeking a scientist to join a program to understand how neuron types from different brain regions are connected and whose activity underlies complex behavior and decision-making. The ideal candidate will be focused on scientific and technical excellence, highly motivated, agile, and team oriented. 

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 

  • Collaborate with a team of scientists and engineers to build and develop an analysis pipeline for large-scale light-sheet microscopy 

  • Analyze large-scale datasets with the goal of understanding the mechanisms of multi-regional neural communication 

  • Deploy large-scale data analysis pipelines on cluster and cloud-based architectures 

  • Pilot new methods for aligning, stitching, fusing, and compressing multi-terabyte scale imaging datasets 

  • Train others to perform novel procedures 

  • Present results internally, via talks and progress reports, and to the external community, via conferences and publications 

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 computer science, biology, biomedical engineering, or related field; or equivalent combination of degree and experience 

  • Demonstrated proficiency in developing large-scale image analysis pipelines 

  • Experience with scaling software from local to cluster or cloud service rodent behavioral experiments or brain tissue processing approaches 

Preferred Education and Experience 

  • 0-4 years of postdoctoral experience 

  • Experience with cluster-based computing (e.g. Spark) 

  • Experience with cloud-based computing (e.g. Amazon S3, Lambda, EMR) 

  • Experience working with terabyte-scale datasets 

  • Excellent written and verbal communication skills 

  • Strong publication record 

  • Ability to write high-quality, reusable code in Python or Matlab 

  • Familiarity with modern software development best practices (e.g., git, GitHub) 

Work Environment 

  • May enter laboratory environment, including possible exposure to chemical, biological, or other hazardous substances 

Physical Demands 

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

  • Frequently required to sit, stand, walk, stoop, kneel, or reach 

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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