Research

Products & Tools

Serving the scientific community is at the center of our mission to accelerate progress toward understanding the brain. We use our unique approach to generate powerful online resources that enable scientists to investigate gene expression, connectivity, single cell morphology, electrophysiology data and more from both mouse and human brains. We also strive to share our research tools, both biological and computational, with the scientific community.

Online Public Resources

More than 50,000 scientists from around the world visit our freely available resources at brain-map.org every month, totaling over two million visitors to date.

We pride ourselves on our open science approach, publishing data online as soon as they pass our quality standards, and often before we publish on it ourselves. Our work has culminated in landmark papers in Nature and other high profile publications, but our first priority has always been to share the data with researchers around the world in order to benefit the entire field.

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Our most recent tool, the Allen Brain Observatory, allows researchers to investigate how circuits in the mouse brain coordinate while the mouse performs visual tasks, taking in and processing a wide range of visual stimuli. In 2015, we launched the Allen Cell Types Database, which gives users a robust way to investigate the brain’s cell types in multiple data modalities, as well as a comprehensive software package to analyze the data.

We also take on other significant projects related to the study and understanding of the brain. These projects include a variety of government-funded research programs and unique collaborations with other partner organizations and scientists who share our desire to fuel new discoveries in neuroscience through an open data model.

Our entire suite of online public resources—each a groundbreaking creation—is available through the Allen Brain Atlas data portal.

Each Allen Brain Atlas resource integrates data from thousands of experiments, yielding unprecedented 3D reference spaces for genetic and anatomic information about the human and mouse brains. Building off our earliest mouse and human brain atlases, we moved on to create further atlases that allow users to explore the developing mouse and human brains as well as the intricate neural connections in the mouse brain. Our newest tools, the Allen Brain Observatory and the Allen Cell Types Database, further expand our portfolio of online resources.

Open Science Research Tools

When our scientists create new biologic materials, software, or specialized devices, we seek to make these tools broadly accessible through openly-available repositories and websites or through collaborations with partners who can develop and broadly distribute our innovations. We are passionate about open science and our goal is for these tools to serve as a trusted resource for the scientific community and spark further cutting-edge discoveries.

Biologic materials

We offer a number of different biological materials that are available for use by the not-for-profit scientific community:

  • Cell-type-specific genetically engineered mice are available through The Jackson Laboratory

  • Genetically engineered plasmids are available through Addgene

  • Genetically engineered adeno-associated viral vectors are available through Penn Vector Core

If you are a for-profit company and you would like to use any of our biological materials, please contact materials@alleninstitute.org.  We do our best to make our biological materials available to commercial entities for internal research purposes, but please be advised that third-party restrictions on component materials may impact our ability to share certain biological materials.

Hardware

We are working to make hardware designs and tools available for those who want to use them to replicate our work or adapt them to their own research. For example, the manuals, parts list, parts files and associated software for a precise automated craniotomy tool is available at autosurgery.org (developed in conjunction with MIT). We will continue to explore ways to share the hardware tools in meaningful, practical ways to help accelerate the progress of other scientists.

Software

The Allen Institute Github page hosts open-source software packages that support public access to Allen Institute resources and data sets. Software available includes:

  • Allen SDK – The Allen Software Development Kit houses source code for reading and processing Allen Brain Atlas data. For the initial release, the Allen SDK focuses primarily on the Allen Cell Types Database. Functionality relevant to other atlases is planned for future releases.
  • DiPDE – DiPDE is a simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. Instead of solving the subthreshold dynamics of individual model leaky-integrate-and-fire (LIF) neurons, DiPDE models the voltage distribution of a population of neurons with a single population density equation. In this way, DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.
  • Vaa3D - Vaa3D is a versatile 3D/4D/5D image visualization and analysis system for bioimages and surface objects (developed in conjunction with HHMI-Janelia).

Community engagement

  • BigNeuron is a community effort to define and advance state-of-the-art of single neuron reconstruction: an essential unsolved challenge in brain science. The project will both standardize the methods to generate high quality and consistent data, and mobilize the reconstruction community to generate interest in solving these complex and interesting algorithmic problems. For more information and to learn how to participate, visit their website.
  • Mozak is a scientific discovery game about neuroscience. The citizen-science project was created by the University of Washington’s Center for Game Science in partnership with the Allen Institute for Brain Science. For more information, visit their website.