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The Allen Cell Types Database contains morphological reconstructions generated from bright-field images of biocytin-stained cells. Reconstructions are generated by manually curating the results of an automated segmentation algorithm.  Please see the morphology technical white paper for more details (TODO).

A standard set of morphological features were computed for all reconstructed cells.  A subset of those features are displayed at the top of the cell-specific morphology page:

Feature Name

Description

Max Euclidean Distance

 

Number of Stems

 

Number of Bifurcations

 

Average Contraction

 

Parent:Daughter

 

For a complete list of computed morphological features, please see the morphology technical white paper (TODO).

The API provides programmatic access to the microscopy images used for reconstruction, axis-oriented projections of those images, and morphological reconstructions. Example queries:

  • Find all cells with morphological images
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  • Find projection image IDs for layer 4 spiny cell (TODO)
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  • Download an image from its ID
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  • Find all images used for reconstruction for a layer 4 spiny cell (TODO)
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  • Download an image from the image stack
No Format
  • Find all cells with morphological reconstructions
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  • Find the reconstruction file for one of those cells
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  • Download the reconstruction file

A standard set of morphological features were computed for all reconstructed cells.  A subset of those features are displayed at the top of the cell-specific morphology page:

Feature Name

Description

Max Euclidean Distance

 

Number of Stems

 

Number of Bifurcations

 

Average Contraction

 

Parent:Daughter

 

For a complete list of computed morphological features, please see the morphology technical white paper (TODO).

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  • Download all of the morphology features for Scnn1a cell 313862022

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No Format
 http://api.brain-map.org/api/v2/data/query.xml?
criteria=model::NeuronReconstruction
,rma::criteria,[specimen_id$eq313862022]

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