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The Allen Institute for Brain Science has created biological and analysis tools that we used to develop our open datasets and other resources. We make many tools available to the scientific community. Below is information about tools such as tutorials, transgenic mice, cell lines, hardware designs, software applications, and other utilities.

Each dataset contains technical documentation that describes detailed methods and protocols. Our newest datasets also have protocols available through Questions and feedback related to any of these resources are welcome in our Community Forum.

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.



Engineers at the Allen Institute develop new designs for scientific instruments, that are customized for our research projects.  Whenever possible, we make these designs available to the broader research community. Learn more about custom hardware that has been developed for use in-house, or in partnership with collaborators.


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, access to the Allen Brain Observatory - Visual Coding dataset available through AWS, and many other applications.

How to Reconstruct Neurons in 3D

The Allen Institute and collaborators have developed processes and tools for reconstructing neuron morphologies in 3D. Background on these morphologies and the processes is available here. For more details about the technology solution and reconstruction workflow, review this page

Allen Institue scientists make a variety of computational analysis tools available to the neurscience community via public GitHub repositories. 

These tools include but aren't limited to software for clustering, visualization, mapping and data access.

Explore a selection of these tools via the Computational Analysis Toolbox page. Additional resources can be found at the Allen Institute GitHub space.


Each Allen Brain Map dataset includes a section for self-guided help, and comprehensive technical documentation.  Visit the Allen Institute YouTube channel for a list of webinars and tutorials that are available for selected data portals. The Allen Institute also hosts periodic in-person training, mini-courses and hackathons;  learn more about past and upcoming  events here.  Or, converse with staff scientists through the Allen Brain Map Community Forum. The Forum also has links to training material using Allen Brain Map resources created by other educators - here is a great example from Dr. Juavinett from UC San Diego.

Interested in teaching materials for high school curricula on brain science?  Lesson plans and other free, open resources are available for educators.

Community Tools

Many external institutions, labs, and individuals have developed tools that extend the usability or host the Allen Institute’s resources. We have curated a centralized database of external tools which utilize Allen Brain Map resources to increase accessibility for both internal and external researchers to learn more about navigating and analyzing Allen Brain Map data. The database consists of computational tools, tutorials, as well as data repositories.

Learn more about the community tools which utilize Allen Brain Map Data.