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Scientist - Imaging - Mindscope Program

Department: Optical Physiology

Scientist, 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.

This Scientist will play a key role within the Mindscope program by utilizing the institute’s multiplexed fluorescence in situ hybridization (mFISH) platform to map ex vivo spatial transcriptomic data onto functional, 2-photon calcium imaging data collected in vivoThis position requires a strong background in fluorescence in situ hybridization, microscopy, and/or experimental transcriptomics and a desire to work in a fast-paced, cross-functional team environment consisting of members of Mindscope, Allen Institute for Brain Science, and Allen Institute for Neural Dynamics.  This position serves as a critical role for internally- and grant-funded projects aimed at linking transcriptomic cell type identity to functional roles of neurons in awake-behaving mice.

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 and deploy systems for neuroanatomical imaging with high-throughput microscopy
  • Design, troubleshoot, and optimize hybridization chain reaction (HCR) experimental protocols to improve data quality and increase throughput
  • Lead in defining project goals, independently propose an experimental strategy to achieve those goals, then execute in collaboration with other contributors
  • Design innovative, complex multi-modal experiments and pipelines, including microscopy data analysis workflows
  • Analyze large-scale datasets with the goal of mapping transcriptomic cell identity back onto functional imaging data
  • Train, mentor, and motivate others to perform complex experiments at scale

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 biological sciences, engineering, or related field; or equivalent combination of degree and experience
  • Minimum of 3 years of relevant postdoctoral experience
  • Experience in applying microscopy and/or transcriptomic techniques in the biomedical sciences

Preferred Education and Experience

  • 5 – 9 years of postdoctoral experience
  • Experience in designing, deploying, and using high-throughput systems for spatial transcriptomics
  • Demonstrated experience with fluorescence in situ hybridization techniques (e.g., merFISH, HCR, etc.)
  • Experience in managing complex projects from concept to completion
  • Excellent project management skills
  • Domain-specific knowledge in neuroscience/neuroanatomy
  • Experience with Python programming

Work Environment

  • May enter laboratory environment, including potential exposure to lasers and 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

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

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 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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