Summer Intern – Brain Science / Characterizing microtracts in dense nanoscale neuroanatomy data

Summer Intern – Brain Science / Characterizing microtracts in dense nanoscale neuroanatomy data

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.

We are seeking a summer intern to join the Data & Technology department for the summer of 2025. They will work to investigate the significance of neurite bundling in dense reconstructions of neural tissue. Our team has collected several electron microscopy datasets which describe the anatomy of the brain in fine detail. We have observed a common morphological feature in which axons and dendrites (neurites) tend to bundle together at various spatial scales. However, we understand little about the significance of these “microtracts” — in particular, whether they are composed of specific patterns of cell types. The Summer Intern will build upon our existing tools for describing morphology and cell types to address this gap. The Intern will first build an understanding of morphology via an exploration of tissue in Neuroglancer, learning how to identify axons, dendrites, and other structures, and developing an intuition for how neurites bundle across the datasets. Then, they will quantify these properties programmatically by applying tools from spatial statistics to our established morphology and cell type descriptions, creating a pipeline for quantifying properties like neurite orientation and bundling. Finally, the Summer Intern will apply these tools to understand the cell type composition of microtracts – in particular, for cortical microcolumns and tracts which pass close to the blood-brain barrier.

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.

Applications must be received by January 7, 2025, to be considered.

Educational Objectives

• Develop an understanding of the organization of neural tissue at nanoscale and how to view and annotate in Neuroglancer
• Learn how to quantify properties of morphology using computational tools
• Learn to do statistical analyses and construct reasonable null models from data
• Learn how to create compelling scientific visualizations, of both primary data and concise summaries of statistical findings
• Learn to work with a team to refine scientific questions and the appropriate methods to answer them

Required Knowledge and Experience

• Ability to write code (ideally some experience with Python)
• Multivariate calculus or linear algebra

Applicant Requirements

• Must be enrolled in, or a 2025 graduate of an accredited associate’s, bachelor’s, or master’s degree program
• Must be able to start on either June 9th or June 23rd, 2025 and commit to the full 10-week program
• Must be eligible to work in the United States for the duration of the internship
• Must be 18 years of age or older

Work Environment

• Open Office Environment

Position Type/Expected Hours of Work

• Interns are expected to work 35-40 hours a week throughout the 10-week period
• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with flexibility to work remotely on a limited basis.

Additional Comments

• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**
• **Travel and/or housing stipend available to qualifying interns**

Compensation

• $21.50 per hour (non-negotiable)

Benefits

• Interns will accrue paid sick days and receive a free Seattle transportation card (ORCA Business Passport)

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.