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Informatics and Data Science Intern

Department: 2210 - Informatics and Data Science
Location: Seattle

Title: Fully automated neuron tracing with deep reinforcement learning

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:

Neuron reconstruction from the whole mouse brain image is a tedious work. During past years, there are many automatic neuron tracing algorithms have been published but those algorithms often fail in reconstruction of the distal arbor and dendrite regions. We have exploited the deep reinforcement learning, which is widely used in self-driving research and applications, to build a self-tracing prototype on the binary data. We expect to extend this study to the real mouse brain data and achieve a relative accurate neuron reconstruction that can be used for further analysis, such as morphology analysis, cell type clustering, etc.

Educational Objectives:

  • improve his/her programming skills, especially in C/C++ and python;
  • learn about basic image processing and analysis techniques;
  • familiar with big image visualization and annotation infrastructure, Vaa3D-TeraFly;
  • learn deep learning and apply it on a real study case.


  • 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 17th, 2019 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, 2019.
  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

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