Summer Intern – Brain Science / Connectomic mapping of human white matter at single axon resolution

Summer Intern – Brain Science / Connectomic mapping of human white matter at single axon resolution

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 Neural Coding department for the summer of 2025. They will work to assist in the development of software tools for interacting with, exploring, and disseminating connectomic maps of densely traced, single axons in human white matter. White matter tracts form the essential connections between brain regions and have been extensively studied in human cognition and disease. Current human brain imaging techniques often lack the resolution needed to reveal critical structural features of white matter, such as fiber density, orientation, and microstructural changes, whereas single-axon resolution brain mapping offers unprecedented insight into how subtle changes within white matter contribute to neurological disorders, aging, and individual variations in cognition. The goal of the proposed internship project will be to develop visualizations of qualitative and quantitative analysis of axon features within and across several anatomical white matter areas. The intern will learn to access, explore, and analyze single-axon datasets using programming and open-source tools, such as Python and Neuroglancer, and will work on developing their own data analysis and visualization code to assess correlations among features, such as axon caliber, orientation, and area, and seek to compare the results of their analysis with anatomical and tractography data from other modalities, such as EM connectomics and MRI.

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

• Learn basic human neuroanatomy, with a focus on white matter fiber tracts
• Develop programming proficiency with Python-based image processing and data analysis packages
• Gain experience with visualization and annotation using specialized software, such as VTK and Neuroglancer, for exploration and analysis of large 3D datasets
• Practice scientific collaboration and presentation in a constructive, team-centered environment
• Receive formal and informal advising on career trajectory (e.g., industry, medical school, graduate school)

Required Knowledge and Experience

• Basic programming ability

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

• Laboratory environment - possible exposure to chemical, biological, or other hazardous substances

Position Type/Expected Hours of Work

• Interns are expected to work 35-40 hours a week throughout the 10-week period
• ONSITE (must be consistent with any lab or animal responsibilities in other sections): 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