ALLEN BRAIN ATLAS API

The Allen Cell Types Database provides multimodal single cell characterization data to enable data-driven approaches to cell type classification.

From the API, you can:

Download electrophysiology data in Neurodata Without Borders (NWB) format
Download computed electrophysiology features
Download images of cell morphology images
Download morphological reconstructions in SWC format
Download computed morphology features
Download neuronal models trained on this data set

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 download neuronal model parameters and run your own simulations using stimuli for the experiments or 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.

Examples:

• 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

  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[name$il'*layer 4*'],donor(transgenic_lines),specimen_tags,cell_soma_locations
  ,rma::options[num_rows$eqall]
  

Electrophysiology

All cells in the Allen Cell Types Database have electrophysiological recordings of responses to stimuli from a common set of current injection protocols. Please see the (TODO) electrophysiology technical white paper for details on specimen selection, tissue processing, recording, and quality control.

The Cell Types Database categorizes detailed stimulus protocols into set of high level descriptions:

Stimulus sweeps that pass quality control standards are available for download as Neurodata Without Borders (NWB) files. To find the NWB download link for Rorb cell specimen 320654829, use this query:

http://api.brain-map.org/api/v2/data/query.xml?
criteria=model::Specimen
,rma::criteria,[id$eq320654829]
,rma::include,ephys_result(well_known_files(well_known_file_type[name$eqNWB]))

Please see the Allen SDK pages (LINKS TODO) on perisomatic biophysical models and generalized leaky integrate-and-fire models for details showing how to download these files in the context of neuronal model simulation.

Morphology

Single Cell Neuronal Models