Scientist I - Neural Coding

At the Allen Institute, we accelerate science for a healthier world through large-scale research designed to answer complex questions in biology. Our multidisciplinary teams generate foundational knowledge, tools, and data to understand how the brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. The Brain Science accelerator aims to produce three interlocking resources: cell type atlases, connectomes, and a knowledge platform with powerful analysis tools. Every dataset is freely shared to fuel discoveries worldwide.

About the role

We are seeking a neuroscientist to lead image processing and analysis of large-scale Electron Microscopy (EM) datasets. The Scientist I will oversee EM image processing and participate in analyzing large-scale datasets to study cell types across multiple modalities and their relationship with brain function. This role is essential to the Connectomics Department, contributing to datasets that bridge structure and function in neuroscience.

Examples of related work:

• eLife: Large-scale EM dataset analysis
• eLife: Connectomics research
• Cell: Structural and functional insights
• Nature: Immersive connectomics

Responsibilities

• Collaborate to scale image processing for a high-throughput electron microscopy pipeline toward whole mouse brain datasets.
• Oversee the automated pipeline for 2D stitching and 3D alignment of EM data.
• Work closely with anatomists, physiologists, theoreticians, and modelers to analyze EM data in the context of cell types and interpret relationships between structure and modalities (e.g., molecular and physiological properties).
• Publish and present findings in peer-reviewed journals and scientific conferences.
• Guide teams and coordinate activities within and across institutions, including mentoring junior members.

Requirements

• Ph.D. in Neuroscience, Computer Science, Applied Math, Engineering, or equivalent combination of degree and experience.
• Strong background in image processing.
• Strong programming skills and experience with software engineering best practices (e.g., version control, code reviews).

Preferred Qualifications

• Experience with Python and cloud computing.
• 3–5 years of relevant programming experience.
• Experience in connectomics or related fields.
• Strong publication record.
• Ability to work independently and collaboratively in a multidisciplinary environment to meet aggressive timelines.
• Machine learning experience.
• Excellent verbal and written communication skills.

Work Environment

• Laboratory environment with potential exposure to lasers and biohazards; may require wearing personal protective equipment (PPE).
• Occasional lifting up to 30 pounds.
• Fine motor movements for operating computers and lab equipment; repetitive motion.
• Stooping, bending, crouching, reaching, or climbing ladders.
• Occasional evening and weekend hours may be required.
• Primarily onsite at 615 Westlake Ave N., with limited remote flexibility.
• Occasional travel to partner sites for compliance oversight and attendance at national/international conferences.

Additional Eligibility

• Include a GitHub repository as part of your job application.
• Submit a cover letter with your application.

This opportunity offers relocation assistance and may provide work visa sponsorship.

Pay

Annualized salary range: $86,150 – $106,650. Final salary depends on education, experience, skills, and work location.

Benefits

• Medical, dental, vision, and basic life insurance.
• 401k plan enrollment.
• Paid time off as outlined in the Allen Institute’s Benefits Guide.