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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. and "Human Cell Types" Products.  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).  Human specimens are tagged with Conditions that indicate any donor disease conditions (tumor, epilepsy, none) and years of seizure history, if applicable.

See whitepapers for detailed experimental and annotation information.

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• All cells in the "Mouse Cell Types" Product

  No Format
  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_tags,cell_soma_locations ,rma::options[num_rows$eqall]

• All cells tagged with 'dendrite type - spiny'

  No Format
  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 tagged with 'dendrite type - spiny'annotated to be in layer 4

  No Format
  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, structurestructure[name$il'*layer 4*'],donor(transgenic_lines),specimen_tags[name$eq'dendrite type - spiny'],cell_soma_locations ,rma::options[num_rows$eqall]

• All human cells annotated to be in layer 4

  No Format
  http://api.brain-map.org/api/v2/data/query.xml?criteria= model::Specimen ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'MouseHuman Cell Types'] ,rma::include,structure[name$il'*layer 4*'],donor(transgenic_lines,conditions),specimen_tags,cell_soma_locations ,rma::options[num_rows$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. See the electrophysiology technical whitepaper for details on specimen selection, tissue processing, recording, and quality control.

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