Data Repositories

BIL (Brain Image Library)

Link 

The Brain Image Library (BIL) is a searchable public data repository for large brain image datasets. Each sample is labeled with modality, technique, related organization, organism, method, and structure.

RRID	SCR_017272
Modality	morphology
Allen Resource Utilized	Allen Mouse Brain Atlas, Allen Human Brain Atlas
Author	Biomedical Applications Group at the Pittsburgh Supercomputing Center and the Center for Biological Imaging at the University of Pittsburgh

Blue Brain Cell Atlas

Link 

The Blue Brain Cell Atlas describes the number, types, and positions of cells in all areas of the mouse brain. It provides densities and positions of all excitatory, inhibitory, and neuromodulatory neurons, as well as astrocytes, oligodendrocytes, and microglia in each of the brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, as well as cell positions and types for modeling and visualizing brain areas. The foundational workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access. 

RRID	SCR_019266
Modality	morphology, electrophysiology, gene expression
Allen Resource Utilized	Allen Mouse Brain  Atlas, Allen Institute Common Coordinate Framework
Author	Csaba Erö
Year Released	2018

Brain Architecture Project

Link 

The Brain Architecture Project collects research resources from various databases to form one homogenous portal of interactive tools and resources. The focus of the portal is creating the first brain-wide mesoscopic connectivity diagram. 

RRID	SCR_004283
Modality	gene expression, morphology
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Partha Mitra
Year Released	2008

BrainStars

Link 

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has a genome-wide expression profile at 51 adult mouse CNS regions. 

RRID	SCR_005810
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Reference Atlas
Author	RIKEN Center for Developmental Biology
Year Released	2009

Cellxgene 

Link Relevant Publication 

The cellxgene tool is a web browser for single-cell transcriptomics data. This browser allows the user to visualize over 1 million cells, cross-filter and compare data of interest, and utilize existing analysis software to interact with the data.

RRID	SCR_021059
Software Type	data repository, visualization tool, data analysis
Modality	gene expression
Allen Resource Utilized	Allen Cell Types Database
Author	Chan Zuckerberg Initiative
Year Released	2021

DANDI: Distributed Archives for Neurophysiology Data Integration

Link 

DANDI is a platform for publishing, sharing, and processing neurophysiology data. The archive is a living repository that enables collaboration within and across labs, and contains neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, as well as images from immunostaining experiments.

RRID	SCR_017571
Modality	electrophysiology, gene expression
Allen Resource Utilized	Allen Institute Cell Types Database
Year Released	2019

DBGap

Link 

DBGap, the database of Genotypes and Phenotypes, was developed to store and share the data and results from studies that have investigated the interaction of genotypes and phenotypes in humans. 

RRID	SCR_002709
Modality	human genotype and phenotype
Allen Resource Utilized	Allen Human Brain Atlas, Cell Types Database
Year Released	2006

Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas

Link Relevant Publication

This website visualizes and shares Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). The anatomical labels were digitized based on Allen ontology, and this web interface was created for easy visualization. These labels isolate and identify mouse brain anatomical structures and the open source data sharing feature facilitates the refinement of anatomical labels and data integration within a single anatomical platform.

RRID	SCR_019267
Modality	neuroanatomy
Allen Resource Utilized	Allen Institute Common Coordinate Framework, Allen ontology
Author	Yongsoo Kim
Year Released	2019

Gene Expression Omnibus (Geo) 

Link 

GEO is a public functional genomics data repository with array- and sequence-based data. This data repository also includes tools to help users query as well as download experiments and curated gene expression profiles. 

RRID	SCR_005012
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Atlas
Year Released	2000

Integrated Brain Gene Expression

Link 

Virtual database indexing brain region gene expression data in mice from Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI). 

RRID	SCR_004197
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	FAIR Data Informatics Lab
Year Released	2017

Linked Neuron Data

Link 

Linked Neuron Data provides multiple interactive resources for extracting, integrating, linking, and analyzing brain data and knowledge from multiple scales and multiple data sources. This web tool includes a brain structure visualization tool, a brain association graph, a morphology data repository, as well as a brain knowledge and semantic search engine.

RRID	SCR_003658
Software Type	data repository, data analysis
Modality	gene expression, morphology, neuroanatomy
Allen Resource Utilized	Allen Mouse Brain Atlas, Allen Human Brain Atlas, Allen Developing Mouse Brain Atlas, Allen Developing Human Brain Atlas, Allen Non-Human Primate Atlas
Author	Yi Zeng, Hunagfu Cunqing, Dongsheng Wang, Hongyin Zhu, Tielin Zhang
Year Released	2013

ModelDB

Link 

ModelDB is a curated database of published computational neuroscience models to be openly accessed, downloaded, and tested. Models can be coded in any language and can be viewed before downloading. 

RRID	SCR_007271
Modality	neural systems
Allen Resource Utilized	Allen Institute Cell Types Database
Author	SenseLab Project
Year Released	1998

National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS)

Link Relevant Publication

NIAGADS is a data repository of genotypic data related to Alzheimer’s disease and related dementias (ADRD) and aging. 

RRID	SCR_007314
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Li-San Wang, Gerard Schellenberg, Christian J. Stoeckert, Jr., Adam Naj, Yuk Yee (Fanny) Leung, University of Pennsylvania School of Medicine
Year Released	2018

NeMO: Neuroscience Multi-omic Data Archive

Link Relevant Publication

The NeMO data repository houses omic data from several large-scale brain research projects. NeMO data includes genomic region data, transcription factor data, as well as cytosine and histone modification data.

RRID	SCR_016152
Modality	gene expression
Allen Resource Utilized	Allen Cell Types Database
Author	Owen White, Institute for Genome Sciences, University of Maryland School of Medicine
Year Released	2017

NeuroMorpho

Link 

NeuroMorpho is a curated inventory of digitally reconstructed neurons along with peer-reviewed publications. The format of the neuronal data includes a unique identifier, general information, the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. The data is searchable by species, brain region, cell type, or lab name. 

RRID	SCR_002145
Modality	morphology
Allen Resource Utilized	Allen Institute Cell Types Database, Allen Institute Brain Explorer
Author	Giorgio Ascoli
Year Released	2006

Open Source Brain

Link 

Open Source Brain is a data resource for collaboratively developing and sharing computational models of neural systems. To foster open processing of this data, ModelDB includes facilities to analyze, visualize and transform models into standardized formats (NeuroML and PyNN). 

RRID	SCR_001393
Modality	neural systems
Allen Resource Utilized	Allen Institute Cell Types Database
Author	Nicholas Cain, Padraig Gleeson, Shreejoy Tripathy
Year Released	2022

Recombinase (cre) Activity

Link 

Recombinase (cre) Activity is a curated data platform with all recombinase-containing transgenes and knock-ins developed in mice, creating a comprehensive resource for delineating known activity patterns and searching for relevant mouse resources.

RRID	SCR_006585
Modality	genetics, epigenetics
Allen Resource Utilized	Allen Mouse Brain Reference Atlas

SageBionetworks Portals 

Link 

The SageBionetworks Portals provide web interfaces for research institutions to exchange, share, and publish curated data or other digital resources. 

RRID	SCR_023844
Modality	Alzheimer's Disease, cell types
Allen Resource Utilized	Seattle Alzheimer's Disease Brain Cell Atlas, Cell Types Database
Year Released	2019

Single Cell Portal

Link

The Single Cell Portal (SCP) is both a data hub and a cell visualization tool. The user can search by study or by gene and visualize the data through plots showing cell clusters, gene expression within and across studies, three-dimensional trajectories, and chromosomal rearrangements.

RRID	SCR_014816
Software Type	data repository, visualization tool, data analysis
Modality	gene expression
Allen Resource Utilized	Allen Cell Types Database
Author	Jon Bistline, Eric Weitz, Jean Chang, Vicky Horst, Timothy Tickle

VisiGene Image Browser 

Link 

VisiGene Image Browser is a virtual microscope for viewing in situ images that show where a gene is used in an organism, often down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns, retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection.

RRID	SCR_003341
Software Type	data repository, visualization tool
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Reference Atlas
Author	Jim Kent, Galt Barber

 

 

Disclaimer

This list of third-party tools utilizing Allen Brain Map resources is for informational purposes only and do not constitute an endorsement or approval by Allen Institute of any of the tools or other products, services, or opinions of the associated organizations. Allen Institute bears no responsibility for the accuracy, legality, or content of the external tools or for that of subsequent links. The descriptions of these tools were adapted from their individual websites.