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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 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 or nearby non-fluorescent neurons.
Morphology - reconstruction-quality, 3-D images of the complete structure of neurons filled and recorded from in vitro slice preparations and 3-D reconstructions of the dendrites and the initial part of the axon and/or the full axon of each neuron.
Transcriptomics - RNA sequencing data derived from single cells isolated from the dorsal part of the lateral geniculate complex (LGd), the primary visual area (VISp) and the anterior lateral motor area (ALM). Single-cell transcriptomics was achieved by using Cre-driven labeling and fluorescence-guided cell selection by FACS.
Generalized Leaky Integrate-and-Fire (GLIF) models - A series of point neuron models of increasing complexity to reproduce the spiking behaviors of the recorded neurons. Starting with a leaky integrate and fire model, more complex models attempt to model variable spike threshold, afterspike currents, and threshold adaptation.
Biophysical-Perisomatic model - compartmental model of neurons that accounts for the neural morphology and emulates electrophysiological responses by assuming biophysically detailed mechanisms for specific families of ionic conductances, with passive dendrites and active conductances at the soma.
Biophysical-All Active model - compartmental model of neurons that accounts for the neural morphology and emulates electrophysiological responses by assuming biophysically detailed mechanisms for specific families of ionic conductances, with active conductances everywhere.

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 and axonal morphologies with annotation of neuronal compartments and extracted quantitative values for each reconstruction.
• RNA sequencing data derived from the LGd, VISp and ALM
• Search and visualization tools for exploring the single cell transcriptomics for LGd, and single cell electrophysiology, morphology, and modeling data.
• 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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