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Scientist II - Machine Learning - Brain Science

Department: Neural Coding

Scientist II – Machine Learning in 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 (for example,

We are seeking a scientist to work as a part of an integrated team of scientists and engineers to develop scalable analysis methods to describe biologically meaningful patterns and phenomena in large-scale electron microscopy datasets. The scientist will research, develop and implement analysis workflows, including developing machine learning models. This will include developing conceptual approaches, executing data cleaning workflows, developing models and training regimens, and executing these approaches across large-scale data. The scientist will communicate their work to a variety of internal and external stakeholders in the form of written and oral presentations including contributing to scientific publications highlighting the biological insights extracted from the data. The scientist will contribute to making the results of their work accessible to others within the team and external to the institute via contribution to open-source software in order to multiply the impact of the data and their work.

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 analysis methods and machine learning models to automate the extraction of biological knowledge from large electron microscopy volumes.
  • Write and deliver reports, presentations, and publications that summarize their work and scientific findings within the dataset

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, computer science, physics, neuroscience, engineering, or other discipline related to essential functions; or equivalent combination of degree and experience
  • Minimum of 3 years of relevant work or research experience
  • Demonstrated effectiveness at team-oriented or collaborative work
  • Demonstrated ability to develop a complex quantitative analysis of neural data, including familiarity with modern machine learning methods
  • Experience with python and common scientific data analysis and visualization packages

Preferred Education and Experience

  • 5 - 7 years of relevant postdoctoral or industrial experience
  • Working knowledge of version control software, such as Git
  • Experience with the dissemination of open-source resources

Physical Demands

  • Occasional lifting up to 30 pounds
  • Frequently required to sit, stand, or walk
  • Fine motor movements in fingers/hands to operate computers and other office equipment; lab equipment

Position Type/ Expected Hours of Work

  • This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.


  • Attendance and participation in national and international conferences required

Additional Eligibility Qualifications

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

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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