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Human Cell Types Intern - Characterizing morphological features between synaptically connected pairs of human cortical neurons

Department: 2520- Human Cell Types
Location: Seattle


Characterizing morphological features between synaptically connected pairs of human cortical neurons

Project Overview:

To understand how our cortex works, it is crucial to understand how its components communicate with each other to generate useful network functions especially between identified cell types. The Institute has devoted a major effort to classifying cell types in human cortex, using multiple large-scale single cell analysis techniques, including transcriptomics, cellular morphology and intrinsic membrane properties. In parallel, we are also able to identify local synaptic connectivity between human cortical neurons with their cell type identity. In this project, we will investigate the morphological properties of connected pairs of human cortical neurons.

For example,

  1. Do the number of putative synaptic contacts depend upon pre- and postsynaptic cell class/type identities?
  2. Are there morphological feature differences between uni-directionally connected pairs compared to bi-directionally (reciprocally) connected pairs within the same cell class/type?
  3. Does dendritic spine density and local presynaptic axonal arborization predict synaptic connection when compared between connected and non-connected pairs of neurons?
  4. Do gap-junctionally connected interneuron pairs have distinct morphological features compared to non-gap-junctionally connected neurons?

We will use these data to extract morphological features to support and/or predict connectivity rules between defined cell types of human columnar microcircuits.

Educational Objectives:

Human cellular morphology data from our Cell Types database ( will be used to compare cortical cell morphology between neurons assayed by multi-patch synaptic connectivity recordings (e.g. dendritic arborization, spines density, axonal morphology, and so on).

Techniques- Learn how to generate and analyze morphological reconstructions (e.g. using Neurolucida and/or Vaa3D software packages), perform morphological analysis (e.g. †using MATLAB) and feature extraction/classification analysis (e.g. MATLAB, Python or R).

Knowledge- Learn about functional roles of morphological cell types in cortex (e.g. spiny and aspiny, layer-specific, axonal projection specific, and so on), and anatomical features between connected pair of human cortical neurons.


  • 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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