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Allen Cell Types Database

This is the online help for the ALLEN Cell Types Database web application.

The Dataset

The Allen Cell Types dataset is a database of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification and is fully integrated with the other Allen Brain Atlas resources.

The Allen Cell Types Database currently includes:


  • Electrophysiology: whole cell current clamp recordings made from identified, fluorescent Cre-positive neurons.
    • Morphology: reconstruction-quality, 3-D wide-field images of the complete structure of neurons filled and recorded from visual cortex in an in vitro slice preparation and 3-D reconstructions of the dendrites and the initial part of the axon of each neuron.
    • Generalized Leaky Integrate-and-Fire (GLIF) models: for neurons with electrophysiological recordings in a battery of stimuli, leaky integrate and fire neuron models and two generalizations are optimized. The generalizations include the presence of afterspike currents and biological reset rules. The optimization methods focus on reproducing only the spike times of these neurons, by minimizing the distance between modeled and observed spike times or maximizing the likelihood of observing the real spike time in a noisy model.
    • “Biophysical” models: compartmental models of neurons that account for the neural morphology and emulate electrophysiological responses by assuming biophysically detailed mechanisms for specific families of ionic conductances.

• Key features
• Registration to the mouse CCF, a 3-D anatomical framework with 3-D structural annotations.
• Data traces for the electrophysiology data from each neuron.
• Manually corrected and curated dendritic morphologies with annotation of neuronal compartments and extracted quantitative values for each reconstruction.
• Search and visualization tools for exploring the single cell electrophysiology, morphology, and modeling data.

Key features

  • Electrophysiological characterization of intrinsic firing properties based on whole cell current clamp recordings
  • Image data and morphological reconstruction of dendritic tree and initial part of the axon based on biocytin fill
  • A variety of abstract point models and more biophysical detailed compartmental models
  • Data and models available for download via Allen Brain Atlas API and Allen Software Development Kit (SDK)

For complete details please see the white papers on our Documentation page.

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