physiology & morphology RNA-Seq Download Documentation Help

Access Physiology and Morphology Data and Models

Electrophysiology recordings, morphology image data, 3D reconstruction and neuronal model parameters for a cell can be downloaded from links from the cell's electrophysiology and morphology pages. Example pages for a Somatostatin (Sst) cell with both perisomatic biophysical and generalized leaky integrate-and-fire (GLIF) models:

Programmatic Access

All data can be programmatically accessed via the Allen Brain Atlas Application Programming Interface (API). There are example queries specific to the Cell Types Database available to help you get started.

Run Models

The accompanying Allen Software Development Kit (SDK) provides code for accessing electrophysiology data in the Neurodata Without Borders file format. Neuronal reconstruction files are available as SWC files. The Allen SDK also provides sample code demonstrating how to download neuronal model parameters and run your own simulations. All biophysical models require NEURON to be installed, whereas the GLIF models use a custom Python simulator included in the SDK.