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Morphology and 3D Reconstruction Intern - Single cell projectome: Using brainwide morphology to understand brain organization

Department: 3300- Morphology and 3D Reconstruction
Location: Seattle


Single cell projectome: Using brainwide morphology to understand brain organization

Project Overview:

By leveraging the recent technology, fluorescence micro-optical sectioning tomography (fMOST) combined with sparse labeling of genetically-identified cortical neurons, we aim to characterize the features of local and long-range axons and dendrites of excitatory and inhibitory neurons in mouse visual cortex and begin to explore how they contribute to our understanding of cortical cell types. The complete, brainwide morphology of individual neurons has only recently become available in the field and we are very excited to see how it can enrich our knowledge about cortical circuits. Whole brain morphology data will also be compared to morphology data generated in an acute slice preparation to identify features common to both datasets (Available on our cell types database Analyzing the morphology of the less well known, long range inhibitory neurons will be of particular interest for this project.

Educational Objectives:

  • Learn cortical neuroanatomy and morphology and how it relates to neuronal cell classes
  • Learn to generate and analyze image-based 3D neuron reconstructions using Vaa3D and Mozak software
  • Learn cutting edge methods for the multi-dimensional characterization of cell types, including the Patch-seq method, FMOST imaging and image processing and pipelines
  • Gain an understanding of the importance and challenges related to understanding cell types, in particular synthesizing results generated using diverse techniques


  • 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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