Scientist I – Advanced Light Microscopy

Allen Institute; Seattle (WA); On-site; USD 87,000 - 108,000; Full time

Benefits offered by this job

Relocation assistance

Possible visa sponsorship

Job summary

The Allen Institute in Seattle seeks a Scientist to design, build, and optimize next-generation light microscopy systems, focusing on light-sheet and expansion microscopy. You will collaborate across biology, engineering, and data science to image large datasets and extract biological insights.

Required PhD with deep optics expertise; strong software and publication record; willingness to work in a lab with lasers. Relocation and visa sponsorship may be available. Term through Sept 2029.

Qualifications

• PhD in physics, optics/photonics, bioengineering, neuroscience, biophysics, or related field.
• Strong expertise in optics and light microscopy with hands-on assembly.
• Experience with expansion microscopy.
• Experience writing software for hardware control and instrument automation (Python).
• Experience in image processing and handling large imaging datasets.
• Experience with light-sheet microscopy.
• Experience with cloud or HPC infrastructure.
• Excellent written and verbal communication; strong publication record.
• May work in laboratory environments with lasers and biohazards.

Responsibilities

• Design, build, align, and characterize custom light microscopy systems
• Optimize imaging performance for expanded specimens
• Prepare biological specimens for imaging, including tissue expansion and labeling workflows
• Operate microscopes to acquire large-scale imaging datasets
• Analyze imaging data to extract quantitative biological insights and develop workflows
• Collaborate with biologists to translate scientific needs into instrument and workflow improvements
• Document protocols, system designs, and analysis methods for reproducibility
• Present results internally and at conferences/publications

Skills

Optics & light microscopy

Expansion microscopy

Python / hardware control

Image processing / data analysis

Large imaging datasets

Light-sheet microscopy

Cloud / HPC

Written & verbal communication

Publication record

Lab safety with lasers

Education

PhD in physics, optics/photonics, bioengineering, neuroscience, biophysics, or related field

Job description

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

The goal of the Neural Dynamics accelerator is to understand how the brain generates flexible behavior. We aim to uncover the algorithms—implemented by dynamics in brain-wide neural circuits—that allow animals to build internal models, process information, and choose actions.

We are searching for a Scientist to help build next-generation light microscopy systems, predominantly light-sheet microscopes, and to use them to image expanded tissue. The ideal candidate will be team-oriented, with deep expertise in optics and microscopy, hands-on experience with expansion microscopy and tissue labeling, and enthusiasm for working across the full imaging pipeline. You will design, build, align, and optimize custom microscopes; prepare specimens for imaging; acquire large datasets; and analyze them to extract biological insight. This position requires close collaboration with biologists, engineers, and data scientists to ensure that new instruments are both technically excellent and scientifically productive.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.
This is a limited term position expected to last through September 2029, with the possibility of extending based on project goals and funding.

Essential Functions

• Design, build, align, and characterize custom light microscopy systems
• Optimize imaging performance for expanded specimens
• Prepare biological specimens for imaging, including tissue expansion and labeling workflows
• Operate microscopes to acquire high-quality, large-scale imaging datasets
• Analyze imaging data to extract quantitative biological insights, and develop or adapt analysis workflows as needed
• Collaborate with biologists to translate scientific needs into instrument and workflow improvements
• Document protocols, system designs, and analysis methods to support reproducibility and sharing
• 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 physics, optics/photonics, bioengineering, neuroscience, biophysics, or a related field; or equivalent combination of degree and experience

Preferred Education and Experience

• Deep experience in optics and light microscopy, including hands-on building and alignment of optical systems
• Demonstrated experience with expansion microscopy
• Track record of writing software for hardware control and instrument automation (e.g., acquisition software, device integration, Python, or similar)
• Demonstrated proficiency in conducting collaborative, multidisciplinary research
• Experience writing software for image processing and data analysis, including handling large imaging datasets
• Experience with light-sheet microscopy specifically
• Experience with cloud or high-performance computing infrastructure
• Excellent written and verbal communication skills
• Strong publication record
• May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

• Fine motor movements in fingers/hands to operate computers, optical components, and laboratory equipment; repetitive motion with lab equipment
• Ability to work in a laboratory environment, including with lasers (appropriate training and safety equipment provided), chemicals, and biological specimens
• Ability to work in dimly lit rooms and to lift 10 lbs

Position Type/Expected Hours of Work

• Occasional evening and weekend hours may be required
• This is a limited term position expected to last through September 2029, with the possibility of extending based on project goals and funding.

Travel

• Attendance and participation in national and international conferences required

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer work visa sponsorship**

Annualized Salary Range

• $87,450 - $108,250

* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

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.