Job Openings at the Allen Institute

Are you ready for new challenges and new opportunities? Join our team in Seattle!
Current job opportunities are posted here as they become available.



Scientist I - Analysis of Connectome and Functional Activity

Department: Modeling and Theory

Scientist – Analysis of Connectome and Functional Activity – Mindscope Program


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 MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Scientist to be an essential team member in a BRAIN Initiative-sponsored project aimed at bridging function, connectivity, and cell types of cortical neurons, thus addressing one of the central questions in Neuroscience: how cell types and connectivity of neurons are related to their functional activity.

This position focuses on linking the connectome and morphologies of cortical neurons to their activity in vivo. Central to this mission is the Electron Microscopy (EM) volume of 1 mm3 of the mouse visual cortex obtained by the Allen Institute (see a similar volume at, along with 2-photon calcium imaging recordings of visual responses of the same neurons.

The core responsibility will be to investigate morphological neuron types and connectivity patterns in the EM volume and map them to the functional neuronal types determined by the visual responses and their modulation by motor activity and arousal. This is a data analysis position, and ideal candidates will have experience in areas like sensory physiology analysis, network science, and machine learning.

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

  • In close collaboration with experimentalists and other analysts, work as a team member to analyze neurophysiology and EM data
  • Develop and apply statistical/machine learning tools for linking neural activity of individual cells to their morphological types and individual connectivity
  • Publish/present findings in peer-reviewed journals and at 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, Computer Science, Applied Math or related field; or equivalent combination of degree and experience
  • Strong computational/data analysis skills

Preferred Education and Experience

  • 0 – 3 years of relevant post-doctoral experience
  • Experience in systems neuroscience (especially in vivo neural measurements and/or sensory neuroscience)
  • Proficiency in Python programming
  • Experience in network science
  • Proved track record of scientific excellence and independent thinking

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office 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.

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.





Applicant Tracking System Powered by ClearCompany HRM Applicant Tracking System