Overview
Allen Brain Map Overview
The Allen Institute for Brain Science was established in 2003 with a goal to accelerate neuroscience research worldwide with the release of large-scale, publicly available atlases of the brain. Our research teams continue to conduct investigations into the inner workings of the brain to understand its components and how they come together to drive behavior and make us who we are.
One of our core principles is Open Science: We publicly share all the data, products, and findings from our work. Here on brain-map.org, you’ll find our open data, analysis tools, lab resources, and information about our own research that also uses these publicly available resources. The potential uses of Allen Institute for Brain Science resources, on their own or in combination with your own data, are endless.
Read below to learn about our major datasets and tools to determine which are the best fit for your needs. If you need help, please see the documentation on each dataset page or visit our Community Forum. Interested in teaching with our open data, analysis tools, and other resources? Get started with our resources for educators.
Allen Brain Atlases
The Allen Brain Atlases capture patterns of gene expression across the brain in various species. Learn more and read publications at the Transcriptional Landscape of the Brain Explore page. Example use cases across the atlases include exploration of gene expression and co-expression patterns, expression across networks, changes across developmental stages, comparisons between species, and more.
The Allen Brain Cell (ABC) Atlas provides a platform for visualizing multimodal single cell data across the mammalian brain and aims to empower researchers to explore and analyze multiple whole-brain datasets simultaneously. This open science resource, developed by the Allen Institute as part of the Brain Knowledge Platform, allows unprecedented insights into the enormous diversity of cell types in the brain and where they are. As the Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas, this groundbreaking platform will keep growing, opening up endless possibilities for discoveries and breakthroughs in neuroscience.
The Allen Mouse Brain Atlas is a genome-wide, three-dimensional map of gene expression throughout the adult mouse brain. The atlas comprises cellular resolution in situ hybridization images with comprehensive anatomic coverage that reveal where each gene is expressed in the mouse brain, as well as an integrated suite of powerful data search, visualization tools, and an annotated reference atlas.
The Allen Human Brain Atlas is a unique multi-modal atlas that maps gene expression across the healthy human brain. Key features include an “all genes, all structures” RNA microarray survey that is spatially mapped to an MRI reference space, in situ hybridization image data at cellular resolution for selected genes in targeted brain regions, and an annotated human brain atlas guide. Additional data on selected neurological conditions are available in the Aging, Dementia, TBI Study and Ivy Glioblastoma Database.
Allen Developing Mouse Brain Atlas
The Allen Developing Mouse Brain Atlas is a detailed map of gene expression changes during the development of the brain. The atlas provides a framework to explore both when and where genes are activated in the mouse brain from embryo through adulthood. Informatics data processing enables both spatial search and temporal search. Developmental reference atlases provide additional context to interpret the data. Anatomic and temporal search locates enhanced gene expression in primary brain areas, and manual data annotation allows users to view curated summaries of gene expression in small structures.
The Allen Spinal Cord Atlas is a comprehensive, genome-wide map of gene expression throughout the healthy mouse spinal cord at ages p56 and p4. This resource details gene diversity in the normal spinal cord and provides an essential baseline for understanding how the spinal cord may be altered in disease or injury. The atlas includes image-based in situ hybridization data at cellular resolution for both juvenile (P4) and adult (P56) stages, with anatomic coverage across the full length of the spinal cord, and accompanying histological reference images.
BrainSpan Atlas of the Developing Human Brain
The BrainSpan Atlas of the Developing Human Brain provides a broad and detailed anatomical analysis of gene expression across multiple stages of early human brain development. It includes in situ hybridization, RNA-sequencing, and microarray data, along with supporting neuroanatomical reference materials.
NIH Blueprint Nonhuman Primate Atlas
The NIH Blueprint Non-Human Primate Atlas provides a developmental neuroanatomical framework for exploring the cellular and molecular architecture of the developing postnatal brain of the rhesus macaque.
Allen Cell Types Database
Our researchers are working to define the “parts list” of the brain by cataloging the different types of neurons and other brain cells in the human and mouse brains. Research teams are studying the brain cells’ detailed shapes, their electrical properties and the suite of genes each individual cell turns on and off, all different properties which can define a distinct brain cell type. Example use cases across the Allen Cell Types Database resources include exploring gene expression patterns across cell types, brain regions, and species; comparing cell types across transcriptomic, electrophysiological, and morphological profiles; defining cell types and taxonomies; and matching data to defined cell types. Learn more at the Cell Taxonomies Explore page.
The Allen Cell Types Database contains multi-modal characterization of cells from the adult human and mouse cortex. Key features include single-cell transcriptomics, whole-cell patch clamp recordings, images of biocytin-filled neurons with full 3D digital reconstructions of selected cells, and Patch-seq data combining all three modalities for a subset of cells. Cell type classifications based on transcriptomic, electrophysiological, and/or morphological properties are also included, as well as computational analysis tools. Additional data on synaptic physiology and cell interactions are also available.
The Allen Institute for Brain Science is an organizing center for the NIH's BRAIN Initiative Cell Census Network (BICCN). The goal of the network is to coordinate data generation, analysis, and resources to provide the research community with a comprehensive reference of cell types in human, mouse, and non-human primate brain. The Allen Institute for Brain Science contributes cell type characterization data related to the Allen Cell Types Database; serves the role of the Brain Cell Data Center (BCDC) to coordinate consortium working groups, standards, and infrastructure; and hosts a web portal and searchable inventory of data produced by the BICCN.
Connectivity
To understand the brain, we need to understand not only its building blocks, the cells, but how those building blocks fit together and interact with one another. Example use cases include exploring neural connections at scales ranging from whole brain to sub-cellular and identify projection patterns by cell type. Learn more about our research on the Connectivity Explore page.
Allen Mouse Brain Connectivity Database
The Allen Mouse Brain Connectivity Atlas is a high-resolution map of neuronal projections in the mouse brain. Generated using transgenic mice genetically engineered to target selected neuronal subsets, the atlas provides a comprehensive “wiring diagram” of the brain. Key features include projection pathways in a navigable Common Coordinate Framework and histological reference images.
The MICrONS program includes large-scale electron microscopy to probe connectivity of cortical circuits and cell morphology of the mouse brain, and also includes functional imaging and computational tools. The program seeks to revolutionize machine learning by reverse engineering the algorithms of the brain, with the goal of providing insights into computational principles that underlie cortical function.
Allen Brain Observatory
The Allen Brain Observatory encompasses the first standardized surveys of in vivo physiological activity in the mouse brain. Systematic, quality-controlled experiments were carried out in mice passively viewing diverse visual stimuli or, as of 2021, mice performing a visual change detection task. Key features include calcium responses from multiple cortical visual areas across hundreds of two-photon imaging sessions, and spiking activity from visual cortex, hippocampus, and thalamus across dozens of electrophysiology sessions. Data and advanced analysis modules can be accessed via the AllenSDK. Use cases include exploring how visual signals are represented in the brain, how signals are relayed between brain regions, the roles of different regions and cell types in visual coding, and flexibility of encoding patterns.
Tools
In addition to our publicly available datasets, we also release all the software and tools used in the development of the Allen Brain Map.
Toolkit resources include programmatic access to Allen Institute data, analysis tools and code, lab resources, and other products for implementing Allen Brain Map resources in your work.
The AllenAPI provides the computational neuroscience community with under-the-hood programmatic access to some of the Allen Institute’s vast datasets. The API contains tools to access high-resolution images, 3D gene expression summaries, microarray and RNA-sequencing data, and more features of the Institute’s resources.
The AllenSDK contains a set of Python software libraries that interact with the AllenAPI and enable users to computationally access and analyze selected data. The Allen SDK supports the Allen Brain Observatory, Allen Cell Types Database, Allen Mouse Brain Connectivity Atlas, and our biophysical modeling tools. Additional software tools are available through the Allen Institute GitHub.
Laboratory resources include transgenic mouse lines available through Jackson Labs, viral tracing tools available through Addgene, and schematics to reproduce the Allen Institute's customized experimental setups.
The Allen Institute develops biologically realistic models of mouse visual cortex, single neuron models of mouse and human cortical neurons, and modeling tools based on our own neuronal data. These models and modeling tools can be connected to additional datasets, used to develop new models based on Allen Institute data, and evaluate model performance. Download the modeling tools for the Brain Modeling Toolkit, SONATA data format for brain models, and more.
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