Documentation

The Allen Institute aims to have our open science tools be as usable by the scientific community as possible.

Access documentation for a wide variety of brain map atlases and datasets in this index. Search for relevant content via keywords and category filters.

Learn how to use our tools to their full potential to advance your research.

Filter by Type
Filter by Category
Filtering by:
tag type
Results:
0
Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
FAQ
Genetic Tools Atlas FAQ

Find answers to frequently asked questions about the Genetic Tools Atlas. Learn about viral vectors, transgenic mouse lines, and tool selection.

Genetic Tools Atlas
Documentation
Data Catalog User Guide

Master the Allen Institute Data Catalog with our user guide. Search and access brain research datasets across projects and data modalities.

BKP Data Catalog
Documentation
Genetic Tools Atlas User Guide

Explore the Genetic Tools Atlas to find AAV vectors and transgenic lines. Select optimal genetic tools for your cell-type specific research.

Genetic Tools Atlas
Documentation
ABC Atlas User Guide

Master the ABC Atlas platform with our complete user guide. Learn to navigate cell type taxonomies and explore molecular data across the whole brain.

ABC Atlas
Documentation
Allen Developing Mouse Brain Atlas: Brain Explorer® 3D Viewer

Master Allen Brain Explorer desktop application for 3D visualization. Navigate brain atlases, view gene expression, and create custom visualizations.

Developing Mouse Brain Atlas
API
Connected Services and Pipes

Learn about Connected Services and Pipes with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
Restful Model Access RMA

Learn about Restful Model Access RMA with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
Quantified Data By Structures

Learn about Quantified Data By Structures with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
Documentation
Image Series Details Mouse Spinal Cord

Learn about Image Series Details Mouse Spinal Cord with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Documentation
Search Mouse Spinal Cord

Learn about Search Mouse Spinal Cord with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Documentation
Allen Brain Explorer Beta User Guide

Learn about Allen Brain Explorer Beta User Guide with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Explorer
Documentation
Expression Mask Color Maps

Learn about Expression Mask Color Maps with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Documentation
Transgenic Mouse Lines Allen Brain Observatory

Learn about Transgenic Mouse Lines Allen Brain Observatory with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Observatory
Documentation
Data Visual Coding

Learn about Data Visual Coding with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Observatory
Documentation
Microarray Data For NHP Atlas

Learn about Microarray Data For NHP Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Non-Human Primate (NHP) Atlas
Documentation
High Resolution Image Viewer

Learn about High Resolution Image Viewer with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Documentation
Overview Allen Brain Observatory

Learn about Overview Allen Brain Observatory with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Observatory
Document Collection
Documentation Mouse Spinal Cord

Learn about Documentation Mouse Spinal Cord with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Documentation
In Situ Hybridization ISH Data For NHP Atlas

Learn about In Situ Hybridization ISH Data For NHP Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Non-Human Primate (NHP) Atlas
Document Collection
Allen Brain Explorer Documentation

Learn about Allen Brain Explorer Documentation with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Explorer
SDK
Software Development Kit Allen SDK Allen Brain Observatory

Learn about Software Development Kit Allen SDK Allen Brain Observatory with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Observatory
Documentation
In Situ Hybridization ISH Data For Ivy Glioblastoma Atlas Project

Learn about In Situ Hybridization ISH Data For Ivy Glioblastoma Atlas Project with comprehensive guides and examples from Allen Institute for Brain Science.

Ivy Glioblastoma Atlas Project
API
API For Ivy Glioblastoma Atlas Project

Learn about API For Ivy Glioblastoma Atlas Project with comprehensive guides and examples from Allen Institute for Brain Science.

Ivy Glioblastoma Atlas Project
Documentation
Brainspan In Situ Hybridization ISH Data

Learn about Brainspan In Situ Hybridization ISH Data with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Document Collection
Documentation Brain Observatory

Learn about Documentation Brain Observatory with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Observatory
Reference Atlases
Reference Data For NHP Atlas

Learn about Reference Data For NHP Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Non-Human Primate (NHP) Atlas
Documentation
Brainspan Searching The Developmental Transcriptome

Learn about Brainspan Searching The Developmental Transcriptome with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Documentation
Rna Sequencing Data For Ivy Glioblastoma Atlas Project

Learn about Rna Sequencing Data For Ivy Glioblastoma Atlas Project with comprehensive guides and examples from Allen Institute for Brain Science.

Ivy Glioblastoma Atlas Project
Documentation
Documentation For NHP Atlas

Learn about Documentation For NHP Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Non-Human Primate (NHP) Atlas
Document Collection
Documentation Ivy Glioblastoma Atlas Project

Learn about Documentation Ivy Glioblastoma Atlas Project with comprehensive guides and examples from Allen Institute for Brain Science.

Ivy Glioblastoma Atlas Project
Documentation
Brainspan Downloading Data

Learn about Brainspan Downloading Data with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Documentation
Rna Sequencing Of The Aging Dementia And TBI Project

Learn about Rna Sequencing Of The Aging Dementia And TBI Project with comprehensive guides and examples from Allen Institute for Brain Science.

Aging, Dementia and Traumatic Brain Injury (TBI) Project
Reference Atlases
Developing Human Reference Atlases

Learn about Developing Human Reference Atlases with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
API
Brainspan API Developmental Transcriptome

Learn about Brainspan API Developmental Transcriptome with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Documentation
Brainspan Prenatal LMD Microarray

Learn about Brainspan Prenatal LMD Microarray with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Documentation
Specimens Of The Aging Dementia And TBI Project

Learn about Specimens Of The Aging Dementia And TBI Project with comprehensive guides and examples from Allen Institute for Brain Science.

Aging, Dementia and Traumatic Brain Injury (TBI) Project
Documentation
Human Brain Atlas In Situ Hybridization ISH Data

Learn about Human Brain Atlas In Situ Hybridization ISH Data with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Document Collection
Documentation Brainspan Atlas Of The Developing Human Brain

Learn about Documentation Brainspan Atlas Of The Developing Human Brain with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Documentation
Human Brain Atlas Brain Explorer

Learn about Human Brain Atlas Brain Explorer with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Documentation
Overview Of The Aging Dementia And TBI Project

Learn about Overview Of The Aging Dementia And TBI Project with comprehensive guides and examples from Allen Institute for Brain Science.

Aging, Dementia and Traumatic Brain Injury (TBI) Project
API
Human Brain Atlas API

Learn about Human Brain Atlas API with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Documentation
Human Brain Atlas Microarray Data

Learn about Human Brain Atlas Microarray Data with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Documentation
Human Brain Atlas Magnetic Resonance Images MRI

Learn about Human Brain Atlas Magnetic Resonance Images MRI with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
API
Cell Types Database API

Learn about Cell Types Database API with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types Database
Document Collection
Documentation Aging Dementia And TBI Project

Learn about Documentation Aging Dementia And TBI Project with comprehensive guides and examples from Allen Institute for Brain Science.

Aging, Dementia and Traumatic Brain Injury (TBI) Project
Documentation
Human Brain Atlas Microarray Data Download

Learn about Human Brain Atlas Microarray Data Download with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Documentation
Allen Developing Mouse Brain Atlas Brain Explorer R 3D Viewer

Learn about Allen Developing Mouse Brain Atlas Brain Explorer R 3D Viewer with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Documentation
Cell Types Database Transcriptomics

Learn about Cell Types Database Transcriptomics with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types Database
Document Collection
Documentation Human Brain Atlas

Learn about Documentation Human Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Documentation
Cell Types Database Physiology And Morphology

Learn about Cell Types Database Physiology And Morphology with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types Database
API
API For Allen Developing Mouse Brain Atlas

Learn about API For Allen Developing Mouse Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Documentation
Developmental Anatomic Gene Expression Atlas AGEA

Learn about Developmental Anatomic Gene Expression Atlas AGEA with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Documentation
Allen Developing Mouse Brain Atlas In Situ Hybridization ISH Data

Learn about Allen Developing Mouse Brain Atlas In Situ Hybridization ISH Data with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
API
API For Mouse Brain Atlas

Learn about API For Mouse Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Document Collection
Documentation Cell Types Database

Learn about Documentation Cell Types Database with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types Database
Reference Atlases
Developing Mouse Reference Atlas

Learn about Developing Mouse Reference Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Document Collection
Documentation Allen Developing Mouse Brain Atlas

Learn about Documentation Allen Developing Mouse Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Documentation
In Situ Hybridization ISH Data

Learn about In Situ Hybridization ISH Data with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Documentation
Allen Developing Mouse Brain Atlas Supplementary Data

Learn about Allen Developing Mouse Brain Atlas Supplementary Data with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Documentation
Anatomic Gene Expression Atlas AGEA

Learn about Anatomic Gene Expression Atlas AGEA with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Documentation
How To Brain Explorer

Learn about How To Brain Explorer with comprehensive guides and examples from Allen Institute for Brain Science.

Brain Explorer
Document Collection
Documentation Allen Mouse Brain Atlas

Learn about Documentation Allen Mouse Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Documentation
Related Studies To Mouse Brain Atlas

Learn about Related Studies To Mouse Brain Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Documentation
Projection Dataset

Learn about Projection Dataset with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
API
API Allen Brain Connectivity Atlas

Learn about API Allen Brain Connectivity Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
Documentation
Transgenic Characterization

Learn about Transgenic Characterization with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
Reference Atlases
Reference Data Mouse Connectivity

Learn about Reference Data Mouse Connectivity with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
Documentation
Brain Explorer 3d Viewer

Learn about Brain Explorer 3d Viewer with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
Document Collection
Documentation Mouse Connectivity Atlas

Learn about Documentation Mouse Connectivity Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Connectivity Atlas
API
API Response Formats

Learn about API Response Formats with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
Allen Brain Atlas API RMA Grammar

Learn about Allen Brain Atlas API RMA Grammar with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
RMA Path Syntax

Learn about RMA Path Syntax with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
Service Pipelines

Learn about Service Pipelines with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
API
Allen Brain Atlas API Data Model

Learn about Allen Brain Atlas API Data Model with comprehensive guides and examples from Allen Institute for Brain Science.

Allen Brain Atlas API
Documentation
Reference Atlas Viewing Tools

Learn about Reference Atlas Viewing Tools with comprehensive guides and examples from Allen Institute for Brain Science.

Anatomy Reference Atlases
Reference Atlases
Allen Human Brain Reference Atlas

Learn about Allen Human Brain Reference Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Human Brain Atlas
Reference Atlases
Allen Developing Mouse Brain Reference Atlas

Learn about Allen Developing Mouse Brain Reference Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Developing Mouse Brain Atlas
Reference Atlases
Brainspan Atlas Of The Developing Human

Learn about Brainspan Atlas Of The Developing Human with comprehensive guides and examples from Allen Institute for Brain Science.

BrainSpan Developing Human Brain Atlas
Reference Atlases
Mouse Spinal Cord Reference Atlases

Learn about Mouse Spinal Cord Reference Atlases with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Spinal Cord
Reference Atlases
Adult Mouse Brain Reference Atlas

Learn about Adult Mouse Brain Reference Atlas with comprehensive guides and examples from Allen Institute for Brain Science.

Mouse Brain Atlas
Protocol
Rna Seq Process Controls

Learn about Rna Seq Process Controls with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types & Taxonomies
Protocol
Human Multiple Cortical Areas

Learn about Human Multiple Cortical Areas with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types & Taxonomies
Protocol
Mouse Whole Cortex And Hippocampus

Learn about Mouse Whole Cortex And Hippocampus with comprehensive guides and examples from Allen Institute for Brain Science.

Cell Types & Taxonomies
Protocol
Synaptic Physiology Analysis Methods Quality Control

Learn about Synaptic Physiology Analysis Methods Quality Control with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
Protocol
Synaptic Physiology Analysis Methods Connection Characterization

Learn about Synaptic Physiology Analysis Methods Connection Characterization with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
Protocol
Synaptic Physiology Analysis Methods

Learn about Synaptic Physiology Analysis Methods with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
Protocol
Synaptic Physiology Experimental Methods Experimental Protocol

Learn about Synaptic Physiology Experimental Methods Experimental Protocol with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
Protocol
Synaptic Physiology Experimental Methods Cell Class Targeting

Learn about Synaptic Physiology Experimental Methods Cell Class Targeting with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
Protocol
Synaptic Physiology Experimental Methods

Learn about Synaptic Physiology Experimental Methods with comprehensive guides and examples from Allen Institute for Brain Science.

Connectivity
No results. Please reduce your search parameters.

Have a specific question or need more help? Check out our Community Forum

Become part of a supportive community created by scientists for scientists. Find answer to your own questions and help your colleagues use brain-map resources to their full extend with Community Forum's diverse content.