Allen Cell Types Database

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

The Dataset

The Allen Cell Types Database contains a multimodal characterization of single brain cells by electrophysiology and morphology, as well as single-cell transcriptional data from nuclei or whole cells. These resources enable data-driven approaches to classification and are integrated with other Allen Brain Atlas applications. Data were collected from adult transgenic mice from fluorescent Cre-positive cells or Cre-negative cells, or from adult human neocortical cells.

The Allen Cell Types Database currently includes the following cell characterization datasets for mouse and human cells

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, VIS, and MOs for mouse and from the MTG for human.
• 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.