Products & Tools

About the Allen Brain Map

Serving the scientific community is at the center of our mission to accelerate progress toward understanding the brain. Our unique approach to science allows us to generate powerful, large-scale atlases and other datasets on the mammalian brain that we publish online as soon as they pass our quality standards. Since our first data was published in 2004, these online resources have enabled the global neuroscience community to investigate gene expression, connectivity, single cell morphology, electrophysiology data and more from mouse, human and non-human primate brains.

These data and the research tools we build in the course of our work are publicly available on our data portal, Allen Brain Map.  

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Collaborative initiatives

We host the BRAIN Cell Data Center (BCDC), the central data portal for all data, tools and knowledge generated through the National Institutes of Health’s BRAIN Initiative Cell Census Network, which aims to create comprehensive atlases of mammalian brain cell types.  

We are a member of Neurodata Without Borders, a consortium that aims to standardize neuroscience data to enable open science and data sharing in the neuroscience community through common data formatting, archiving and analysis methods. The consortium’s first project, Neurodata Without Borders: Neurophysiology, is a standardized format and methods for neurophysiology data.  

In collaboration with Baylor College of Medicine, Princeton University and Harvard Medical School, our researchers are contributing to IARPA MICrONS with goals to create the largest ever roadmap of connections in the mammalian brain. Our electron microscopy team is contributing to this enormous effort by imaging billions of tiny synaptic connections in a cubic millimeter of mouse neocortex.


Further details of some of our research tools and resources follow. For more information see the toolkit on the Allen Brain Atlas.

Biological Resources

Transgenic TIGRE mouse lines developed by researchers at the Allen Institute for Brain Science

In the course of our research, we develop several different types of biological tools, many of which we make available for use by the broader research community.  


We helped develop Neuropixels, a new type of silicon probe that allows researchers to record electrical activity from hundreds of neurons at a time in the mouse brain. This collaborative effort involved scientists and engineers at the Howard Hughes Medical Institute’s Janelia Research Campus, the Allen Institute for Brain Science, University College London and imec. 


Together with the Massachusetts Institute of Technology, we developed a method for precise automated craniotomies. The manuals, parts list, parts files and associated software for this tool are available at  


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.  
  • Brain Modeling Toolkit (BMTK) — BMTK is a software package for building and simulating large-scale models of neuronal circuits that enables the computational neuroscience community to build models of the brain at different levels of granularity.  
  • DiPDE –The displacement integro-partial differential equation (DiPDE) is a simulation platform for numerically solving the time evolution of coupled networks of neuronal populations.  
  • Vaa3D - Vaa3D is a versatile 3D/4D/5D image visualization and analysis system for bioimages and surface objects and was developed in conjunction with HHMI-Janelia.