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Cell Taxonomies

The Allen Institute for Brain Science builds data-driven classifications of cell types in the mammalian brain. The datasets and publications below provide insight into organization of the cellular and molecular complexity of this amazing biological system. 

We seek input from the community as we continue to develop tools and paradigms to classify cells, and encourage discourse on the Allen Community Forum.

Transcriptional taxonomy of the mouse cortex

The RNA-Seq Data Navigator is a tool to explore transcriptional data at the level of gene expression, annotated by cell class using a data-driven taxonomy. Transcripts can be viewed based on similarity of expression pattern, or comparisons of cell sample properties.Two areas of the mouse neocortex were analyzed: 14,249 cells were profiled from the primary visual cortex (VISp), and 9,573 cells from the anterior lateral motor cortex (ALM). These two regions represent distant poles of the neocortex and perform distinct functions.

Analysis of these transcriptional profiles reveals 133 transcriptomic cell types, divided into 61 GABAergic neuron types and 16 non-neuronal types, most of which are shared across both cortical areas, and 56 glutamatergic neuron types, most of which segregate by cortical region. 

Gene-level (exon and intron) read counts and metadata for all samples is available at

Transcriptional taxonomy of the human cortex

The RNA-Seq Data Navigator is also designed to explore transcriptional data from human brain, annotated by cell class using a custom taxonomy.  Cell nuclei (15,928 ) were analyzed from 8 human tissue donors, ranging in age from 24-66 years. Analysis of these transcriptional profiles reveals approximately 75 transcriptionally distinct cell types covering multiple cortical areas and laminae, subdivided into 45 inhibitory neuron types, 24 excitatory neuron types, and 6 non-neuronal types.

Gene-level (exon and intron) read counts and metadata for all samples is available at

Interactive tutorial: Building a cellular taxonomy of the mouse visual cortex

The mammalian brain is composed of various cell populations that differ based on their molecular, morphological, electrophysiological and functional characteristics. Classifying these cells into types is one of the essential approaches to defining the diversity of brain’s building blocks. 

An interactive cellular taxonomy visualization representing diversity in the mouse primary visual cortex allows you to browse this landscape, based on gene expression at the single cell level, using data from over 1,600 cells. This visualization will guide you through some of the data and insights from this study.

Explore  | Publication 

Cytosplore Viewer

Cytosplore Viewer is a downloadable application that allows exploration of single cell RNA-Seq data from the Allen Cell Types Database. Currently, Cytosplore Viewer includes sequencing data from over 15,000 nuclei gathered from the human Middle Temporal Gyrus (MTG). It also includes single cell sequencing data of the Primary Visual Cortex (VISp) and Anterior Lateral Motor Cortex (ALM) in mouse brain.  Cytosplore was developed by a team from the Leiden Computational Biology Center, the Division of Image Processing at the Leiden University Medical Center, and the Computer Graphics and Visualization Group at the TU Delft in collaboration with the Allen Institute.


In addition to data navigation tools, researchers at the Allen Institute share data via published peer-reviewed articles and pre-review open access services, to provide insight into the data and analysis used to build taxonomies.  Selected studies are below.

Classification of electrophysiological and morphological neuron types in the mouse visual cortex

To systematically profile morpho-electric properties of mammalian neurons, a single-cell characterization pipeline was built to generate data from patch-clamp recordings in brain slices, and biocytin-based neuronal reconstructions. This article presents the results of that study, with a taxonomy of morphologically and electrophysiologically defined cell types in the mouse cortex: 17 electrophysiological types, 38 morphological types and 46 morpho-electric types.  Data from this publication can be explored in the Allen Cell Types Database


Transcriptional landscape of the prenatal human brain

This manuscript provides a comprehensive view of when and where genes are expressed while the brain is developing, providing insight into the cell progenitor groups that give rise to discrete classes. 

Publication  |  Microarray data

Cell type discovery using single-cell transcriptomics: implications for ontological representation

A review of recent studies of cellular diversity in the human brain and immune system using single cell and single nucleus RNA-sequencing. Discussion of a method to identify cell type specific marker genes and a proposal for naming and representing cell types in a structured Cell Ontology.


Shared and distinct transcriptomic cell types across neocortical areas

This work presents a high resolution cellular taxonomy of two regions of mouse cortex using single cell RNA-sequencing. Data in this work is included in the RNA-Seq Data Navigator tool for mouse, described above.


Conserved cell types with divergent features between human and mouse cortex

This manuscript describes a cellular taxonomy of human cortex using single nucleus RNA-sequencing. Identification of matching cell types and cell classes between human and mouse is provided, and analysis of divergent expression between matching types. Data in this work is included in the RNA-Seq Data Navigator tool for human, described above.