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Informatics and Data Science Intern

Department: 2210 - Informatics and Data Science
Location: Seattle

Title: Automatic neuron reconstruction algorithm evaluation and development for whole mouse brain

Program Overview

Students will be matched with mentors and projects based on degree of experience and mutual interests. In addition to working on a specific project, Allen Institute interns will meet regularly as a group in sessions designed to augment their research experience. These meetings could include sessions aimed at improving communication skills, opportunities to share their projects with peers, and discussions with Allen Institute scientists and staff representing different disciplines within the organization. At the end of the program, each intern will write up a project summary and give a presentation summarizing their work.

Project Summary:

Automatically reconstructing neurons at the whole brain level requires processing trillions of voxels in imaging data of a brain in high speed, which is still a very challenging task. Our group has developed a number of tools/technologies to automate very large-scale whole brain full morphology reconstructions. Our 2019 Summer Intern will learn how to use our common platform Vaa3D software to test/evaluate the performance of different reconstruction algorithms on very large-scale neuron images. With the contribution from our summer intern, our goal is to develop a robust reconstruction framework for the whole mouse brain database.

Educational Objectives:

  • Learn how to use our software Vaa3D including Virtual Reality module for automatic/manual 3D neuron reconstruction.
  • Learn how to develop algorithms and tools for large-scale image/ reconstruction visualization and analysis.
  • Learn C/C++ programing skill.
  • Learn deep learning, image processing, computer vision, and computational biology.


  • U.S. Citizen or U.S. Permanent Resident currently enrolled in an accredited U.S. college or university.
  • Enrolled in undergraduate studies or in a Masterís program. You must be enrolled and returning to school Fall quarter.
  • Must be able to start on June 18th, 2018 and commit to the full 10-12 week internship time period. Interns will be expected to work 35-40 hours a week.
  • Must be 18 years of age or older.


Interns will receive $15.00 per hour which is equivalent to $6,000 less taxes.


Housing is not provided as a part of the internship program. If selected we will provide a list of housing resources for you.


Interns will be provided with an ORCA business passport free of charge for the duration of their internship.

How to Apply

  1. Complete an application through this portal. The application deadline is January 30, 2018.
  2. Submit a resume as well as the following documents using the + supplemental documents button:
    • A personal statement describing your interest in Allen Institute for Brain Science
    • College transcript with Cumulative GPA and Courses taken (can be unofficial)

3. Send one letter of recommendation to

Contact us

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