ALLEN BRAIN ATLAS API
The Allen Cell Types Database provides multimodal single cell characterization data to enable data-driven approaches to cell types classification.
From the API, you can:
Download electrophysiology data in Neurodata Without Border (NWB) format
Download computed electrophysiology features
Download images of cell morphology
Download morphological reconstructions in SWC format
Download computed morphology features
Download neuronal models trained on this dataset
This document provides a brief overview of the data, database organization and example queries. API database object names are in camel case. See the main API Documentation for more information on data models and query syntax.
The accompanying Allen Software Development Kit (SDK) provides python code for accessing electrophysiology data (NWB files) for all cells and morphological reconstructions (SWC files) for a subset of cells. The Allen SDK also provides sample code demonstrating how to do download neuronal model parameters and run your own simulations using stimuli for the experiments of custom current injections.
Experimental Overview And Metadata
Experimental data from Allen Cell Types Database is associated with the "Mouse Cell Types" Product.
Each brain specimen is sectioned in the coronal plane at section thickness of 350 µm. The sections are then hemisected along the midline and a single cell in the hemisected tissue is targeted for electrophysiological recording and biocytin fill to visualize the cell morphology. Each cell is represented as Specimen object.
Each cell Specimen is associated with an anatomical Structure and CellSomaLocation record containing the coordinate of the cell in the Common Coordinate Framework and a normalized depth between pia (value of 0) and white matter (value of 1) surfaces.
Each cell Specimen is also associated with two SpecimenTags describing the “dendrite type” (spiny, aspiny, sparsely spiny) and the “apical dendrite” (intact, truncated, n/a).
See whitepapers for detailed experimental and annotation information.
From the API, detailed information about cells can be obtained using RMA queries.
- All cells in the "Mouse Cell Types" Product
http://api.brain-map.org/api/v2/data/query.xml?criteria= model::Specimen ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types'] ,rma::include,structure,donor(transgenic_lines),specimen_tags,cell_soma_locations ,rma::options[num_rows$eqall]
- All cells tagged with 'dendrite type - spiny'
http://api.brain-map.org/api/v2/data/query.xml?criteria= model::Specimen ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types'] ,rma::include, structure,donor(transgenic_lines),specimen_tags[name$eq'dendrite type - spiny'],cell_soma_locations ,rma::options[num_rows$eqall]
- All cells annotated to be in layer 4