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Modeling, Analysis, and Theory Intern - Retinotopic localization of visually responsive neurons recorded in the Allen Brain Observatory

Department: 2260-Modeling Analysis and Theory
Location: Seattle


Retinotopic localization of visually responsive neurons recorded in the Allen Brain Observatory

Project Overview:

Distinct parts of each visual region respond to different parts of visual space, a phenomenon known as retinotopy. As part of two-photon data collection for the Allen Brain Observatory, the visual cortex is mapped with a technique known as intrinsic signal imaging (ISI), which can be used to create a retinotopic map. However, we currently do not associate the single cells recorded via two-photon imaging with their respective retinotopic location per ISI.† The objective of this project is to establish this association for all neurons released as part of the Allen Brain Observatory, i.e. to assign a segment of visual space to each (visually responsive) neuron that is part of the Allen Brain Observatory public data release.

Depending on the rate of success/progress, as well as the internís interest, the scope of the project can be easily expanded in a multitude of directions. E.g. the intern could correlate various visual response metrics with the retinotopic location of the respective neuron, and attempt to interpret such correlations. Or, alternatively, the intern could investigate if it is possible to predict ISI-retinotopy from two-photon data via machine learning.

Ideally, the candidate should be interested in data analysis, mathematically inclined and have some prior exposure to the Python programming language.

Educational Objectives:

  • Learning about the Allen Brain Observatory
  • Learning about ISI, understanding retinotopic mapping incl. limitation of the technique
  • Learning about two-photon imaging of neural activity
  • Understanding image registration and coordinate transformations
  • Working with Python and the Allen Brain Observatory SDK
  • Running code on the Cluster (HPC)
  • Elements of data science and machine learning (depending on the internís interests)
  • Elements of literature review
  • Elements of public speaking and presentation design in scientific practice


  • 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 either June 3rd or 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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