Atlases and Ontologies



The Blue Brain Cell Atlas is a comprehensive online resource that describes the number, types, and positions of cells in all areas of the mouse brain. The atlas provides the densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of the brain regions defined in the Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. The underlying workflow uses imaging data from the Allen Institute Common Coordinate Framework to generate cell positions and assign their type using the API for data access. (Blue Brain Project, RRID:SCR_002994)

Access the Blue Brain Cell Atlas here:


Blue Brain Project (, EPFL




Neuron Phenotype Ontology - An important aspect in the classification of cell type identity and function is the use of powerful and flexible ontologies. The Neuron Phenotype Ontology is a prototype system for managing neuronal phenotypes that spans across the different phases of knowledge discovery. The system comprises a  knowledge base of neuron types and supporting python codes, and supports the concepts of common usage types and evidence based models. It enables researchers to generate a complex neuron phenotype out of any number of individual phenotypes.  Phenotype values are tied to formal biomedical ontologies, ensuring a consistent semantic representation and that the phenotypes themselves can be integrated with other types of data. Version 1.0 of the ontology is currently available. (NIFSTD, RRID:SCR_005414)

Access the Neuron Phenotype Ontology here:


Neuroscience Information Framework (, University of California, San Diego