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Scientist II – Imaging, Microscopy

Allen Institute
Seattle, Washington State
Commensurate to years of experience
Closing date
May 5, 2021
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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 Imaging Department within the Allen Institute for Brain Science consists of 15-20 scientists who construct and operate brightfield, widefield fluorescence, confocal, light sheet, 2-photon and 3-photon microscopes. The holder of this NIH grant-funded position will spearhead 3-photon microscopy at the Allen Institute.

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

  • Further develop and maintain our 3-photon microscopes at the Allen Institute and the University of Washington
  • Assist collaborators during experiments to monitor neural activity and blood flow in deep layers of neocortex, white matter and hippocampus in mice; cortex in larger mammals; and the brain and peripheral nervous system in drosophila
  • Disseminate microscope designs and procedures through publications, national and international collaborations, and our website

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, physics or related field or equivalent combination of degree and experience required
  • Experience with microscope design and nonlinear optics, including multiphoton microscope design and alignment

Preferred Education and Experience

  • Experience with ultrashort pulses in the near-IR and short wave-IR, including spectral and temporal measurement (e.g. autocorrelation, FROG), and amplitude modulation and compression techniques (e.g. electro-optic modulators, prism and/or grating pre-chirpers)
  • Facility with optical and optomechanical design software (e.g. Solidworks & Zemax)
  • Working knowledge of ScanImage
  • Working knowledge of in vivo calcium imaging analysis, including motion correction, segmentation, neuropil subtraction, trace extraction, ?F/F calculation
  • Experience of and ability to perform multiphoton imaging experiments with awake mice and/or other mammals


Work Environment

  • Laboratory environment, including potential exposure to lasers

Physical Demands

  • 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


  • Travel to partner sites
  • Attendance and participation in national and international conferences required

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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