Allen Cell Types Database
This is the online help for the ALLEN Cell Types Database web application.
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 or nearby non-florescent 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 full or initial part of the axon of each neuron.
Transcriptomics - single-cell RNA Seq was performed on cells from the core and shell regions of LGd from 4 Cre-lines to a depth of 2.4M reads per cell.
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 - a biophysically realistic compartmental model of neurons that account for the neural morphology and emulates electrophysiological responses assuming passive dendrites and active soma.
Biophysical-All Active model - compartment model of neurons that account for the neural morphology and emulates electrophysiological responses assuming active conductances everywhere.
• 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.
• Projection and Intrinsic Signal Imaging sign maps displayed in a Cortical Map Viewer.
• Search and visualization tools for exploring the single cell electrophysiology, morphology, and modeling data.
• Data and models available for download via Allen Brain Atlas API and Allen Software Development Kit (SDK)
• RNA sequencing data derived from single cells isolated from the dorsal part of the lateral geniculate complex (LGd)
For complete details please see the white papers on our Documentation page.