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Single Cell Data and 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.

Morphology and Electrophysiology

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:

Run Neuronal 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.

Transcriptomics Profiling

Single cell and nucleus transcriptomes assayed from human and mouse brain regions are available for download via the links shown below.

Species

Brain Region

Number of Cells or Nuclei

Links to Data

Human

Middle Temporal Gyrus (MTG)

15,928

Gene-level (exonic and intronic) CPM values for all samples (zip)

Mouse

Primary Visual Cortex (VISp)

8,329

Gene-level FPKM values for all samples (zip)

URL to file with expected counts, FPKM and TPM values for each sample. (csv)

Mouse

Anterior Lateral Motor Area (ALM)

5,992

Gene-level FPKM values for all samples (zip)

URL to file with expected counts, FPKM and TPM values for each sample. (csv)

Mouse

Dorsal Lateral Geniculate Complex (LGd)

1,772

RNA-Seq heatmap for LGd

Gene-level FPKM values for all samples (zip)

URL to file with expected counts, FPKM and TPM values for each sample. (csv)

 

Reference genome .gtf files used to align the RNA-sequencing data for mouse (zip) and human (zip).

For more information on the methods involved in this study, please see the Transcriptomics Overview whitepaper in Documentation