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The Allen Cell Types Database constains 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).

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
  • Find projection image IDs for layer 4 spiny cell (TODO)
  • Download an image from its ID
  • Find all images used for reconstruction for a layer 4 spiny cell (TODO)
  • Download an image from the image stack
  • Find all cells with morphological reconstructions
  • Find the reconstruction file for one of those cells
  • Download the reconstruction file Image Added
    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


    Max Euclidean Distance


    Number of Stems


    Number of Bifurcations


    Average Contraction




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

To download all of the morphology features for Scnn1a cell 313862022:

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Single Cell Neuronal Models