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The Allen Institute for Brain Science has created biological reagents and analysis tools necessary to develop our datasets and open resources.  We strive to make these tools available to the scientific community. Tutorials and webinars are available via the Allen Institute for Brain Science YouTube channel.  Below is information about resources such as transgenic mice, cell lines, downloadable software, and other utilities.   

Biological Resources

Transgenic Mouse Lines

The Allen Institute has generated over 100 transgenic mouse lines for cell-type-specific labeling and manipulation.  These lines are made available through The Jackson Laboratory.  Learn more about the driver and reporter lines, and access characterization data that is available.

Viral tools

Viral transfection is often used in a molecular toolkit to modify neurons; the Allen Institute for Brain Science uses viruses to target and label specific classes of neurons for further study. A variety of different viruses have been generated and are available to the community. Learn more about viral reagents used in our molecular profiling research.

Human Embryonic Stem Cell Lines

The Allen Institute has generated a variety of human embryonic stem cell lines that report the expression of selected genes, or cause the disruption of target genes.  These lines are now available through WiCell's Allen Institute Stem Cell Collection for Early Human Brain Development.


Several Allen Brain Atlas datasets include Magnetic Resonant Imaging (MRI), Diffusion Tensor (DT) and Computed Tomography (CT) scan data that are open and downloadable. Learn more about the types of molecular imaging data available through these resources.




The Allen Software Development Kit (SDK) contains a set of software libraries that interact with the API and enable users to easily read and analyze the data and tools portfolio of the Allen Brain Atlas. The Allen SDK includes utilities for the Allen Cell Types Database, including source code for downloading and running simulations of Generalized LIF and perisomatic biophysical neuronal models.  Data from the Allen Brain Observatory is also accessible via the SDK.



The Allen Institute Github space hosts software packages that use or support access to online projects, resources, publications and data sets affiliated with the Allen Institute.  This includes the AllenSDK, the Brain Modeling Toolkit (bmtk), the DiPDE model simulation platform, and many other applications.

Visit the Allen Institute YouTube channel for a list of webinars and tutorials that are available for selected data portals.