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Tutorials & How-To's

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

Access tutorials and how-to resources 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 with step-by-step walkthroughs and guidance.

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Onboarding
Download a file manifest for all female chimpanzees from Ed Lein’s - UM1MH130981 BICAN grant

Learn to download file manifests for female chimpanzee brain data from the BICAN grant. Access primate neuroscience research datasets.

Onboarding
Onboarding
Use BKP file manifest to access BICAN data at NeMO archive

Learn to access BICAN consortium data at NEMO Archive using BKP file manifests. Efficiently download large-scale brain research datasets.

Onboarding
Onboarding
Finding AAVs for targeting Cholinergic cell populations in the striatum

Discover how to find AAV vectors for targeting cholinergic neurons in the striatum. Learn viral vector selection for precise cell targeting.

Onboarding
Onboarding
Guided exploration of ASAP-PMDBS data in the ABC Atlas

Take a guided tour of ASAP-PMDB Parkinson's disease data in the ABC Atlas. Explore molecular profiles and pathology across brain regions.

Onboarding
Video
Allen Mouse Brain Atlas

Watch this complete video tutorial on Allen Mouse Brain Atlas. Learn gene expression search, ISH image viewing, and anatomical navigation.

Video
Video
Allen Brain Observatory

Watch this comprehensive video tutorial on using Allen Brain Observatory. Learn to navigate visual coding datasets and analyze neural activity recordings.

Video
API
Atlas Drawing and Ontologies

Explore how brain atlases are created and organized through ontologies. Learn about anatomical structure hierarchies and classification systems.

API
API
Image-to-Image Synchronization

Master image-to-image synchronization for comparing brain atlas data. Navigate corresponding sections across multiple datasets simultaneously.

API
API
Downloading 3-D Expression Grid Data

Learn to download 3-D expression grid data as NRRD files. Access voxel-level gene expression values for computational brain analysis.

API
Video
Allen Human Brain Atlas

Follow this video guide to master Allen Human Brain Atlas. Learn to search genes, explore expression patterns, and navigate human brain anatomy.

Video
API
Downloading a WellKnownFile

Discover how to download .well-known files from Allen Institute resources. Access metadata and configuration information for data integration.

API
API
Downloading and Displaying SVG

Learn to download and display SVG graphics from Allen Brain Atlas. Work with scalable anatomical diagrams for research and presentations.

API
API
Downloading an Ontology's Structure Graph

Download ontology structure graphs showing brain anatomy hierarchies. Access anatomical structure relationships and organizational data.

API
API
Downloading an Image

Learn to download high-resolution brain images from Allen Institute. Access ISH images, atlas sections, and microscopy data with quality options.

API
Onboarding
MapMyCells Use case: single cell genomics in mouse

Use MapMyCells to map mouse single-cell genomics data to Allen taxonomies. Classify your cells using reference transcriptomics data.

Onboarding
Onboarding
MapMyCells Use case: single nucleus RNA-seq from human MTG

Map human MTG single nucleus RNA-seq data using MapMyCells. Classify cells against Allen human brain reference taxonomies.

Onboarding
Onboarding
Step-by-step guide to using MapMyCells

Follow this complete guide to using MapMyCells. Learn data upload, cell mapping to taxonomies, result interpretation, and downloads.

Onboarding
Video
Cell Type Taxonomies Webinar Series

Join our webinar series on cell type taxonomies. Learn about brain cell classification from single-cell transcriptomics and taxonomy development.

Video
Onboarding
Intro to the Adult Mouse Atlas

Get started with Allen Adult Mouse Atlas. Learn basic navigation, gene expression search, and how to explore mouse brain anatomy.

Onboarding
Video
Cell Type Knowledge Explorer video tutorial

Watch this video guide to Cell Type Knowledge Explorer. Learn to navigate single-cell data and explore cell type classifications and marker genes.

Video
Education
A Course-based Research Experience Using Allen Brain Map

Discover how to create an engaging course-based research experience using Allen Brain Map. This tutorial helps educators integrate real neuroscience data into their curriculum.

Education
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