These tools are organized by a description of their functionality, their RRID (Research Resource Identification), data modality, and which Allen Institute resource's data was utilized for this tool. The authors of the tool are listed first by computational contributors then by academic authors when the tool has a relevant publication.
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 | |
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 |
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 |
|
Modality |
morphology, electrophysiology, gene expression |
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Institute Common Coordinate Framework |
Author |
Csaba Erö |
Year Released |
2018 |
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 |
|
Modality |
gene expression, morphology |
Allen Resource Utilized |
Allen Mouse Brain Atlas |
Author |
Partha Mitra |
Year Released |
2008 |
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 |
|
Modality |
gene expression |
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
Author |
RIKEN Center for Developmental Biology |
Year Released |
2009 |
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 |
|
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 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 | |
Modality |
electrophysiology, gene expression |
Allen Resource Utilized |
Allen Institute Cell Types Database |
Year Released |
2019 |
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 |
|
Modality |
human genotype and phenotype |
Allen Resource Utilized |
Allen Human Brain Atlas, Cell Types Database |
Year Released |
2006 |
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 |
|
Modality |
neuroanatomy |
Allen Resource Utilized |
Allen Institute Common Coordinate Framework, Allen ontology |
Author |
Yongsoo Kim |
Year Released |
2019 |
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 |
|
Modality |
gene expression |
Allen Resource Utilized |
Allen Mouse Brain Atlas |
Year Released |
2000 |
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 |
|
Modality |
gene expression |
Allen Resource Utilized |
Allen Mouse Brain Atlas |
Author |
FAIR Data Informatics Lab |
Year Released |
2017 |
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 |
|
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 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 |
|
Modality |
neural systems |
Allen Resource Utilized |
Allen Institute Cell Types Database |
Author |
SenseLab Project |
Year Released |
1998 |
NIAGADS is a data repository of genotypic data related to Alzheimer’s disease and related dementias (ADRD) and aging.
RRID |
|
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 |
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 |
|
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 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 | |
Modality |
morphology |
Allen Resource Utilized |
Allen Institute Cell Types Database, Allen Institute Brain Explorer |
Author |
Giorgio Ascoli |
Year Released |
2006 |
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 |
|
Modality |
neural systems |
Allen Resource Utilized |
Allen Institute Cell Types Database |
Author |
Nicholas Cain, Padraig Gleeson, Shreejoy Tripathy |
Year Released |
2022 |
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 |
|
Modality |
genetics, epigenetics |
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
The SageBionetworks Portals provide web interfaces for research institutions to exchange, share, and publish curated data or other digital resources.
RRID |
|
Modality |
Alzheimer's Disease, cell types |
Allen Resource Utilized |
Seattle Alzheimer's Disease Brain Cell Atlas, Cell Types Database |
Year Released |
2019 |
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 |
|
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 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 |
|
Software Type |
data repository, visualization tool |
Modality |
gene expression |
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
Author |
Jim Kent, Galt Barber |
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.
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