Visualization Tools
Visualization Tools
These tools are organized by a description of their functionality, their RRID (Research Resource Identification), the type of software, 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.
3DBAR: The 3D Atlas Brain Reconstructor
3DBARs contains a repository of digital representations of different brain atlases and a repository of 3D models of brain structures to create visualizations for the user. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites.
|
RRID |
|
|
Software Type |
Data analysis software, visualization tool |
|
Modality |
Neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Piotr Majka, Jakub Dzik |
Allen Brain Atlas-Driven Visualizations
ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures. This tool utilizes Data-Driven Documents (D3), a Javascript library that uses data to drive the creation and control of visualizations in web browsers. ABADV allows researchers to immediately obtain and survey mouse gene expression data using a variety of visualizations, which can then be used to supplement their work or perform meta-analysis.
|
RRID |
|
|
Software Type |
visualization tool |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Andrew Zaldivar, Michael Beyeler |
|
Year Released |
2014 |
AllenDigger
AllenDigger is a toolkit to preprocess gene expression data and visualize the spatial distribution of genes of interest, characterize the spatial heterogeneity of the brain, as well as to register cells from single-cell transcriptomics data to fine anatomical brain regions via machine learning methods. AllenDigger aids precise spatial gene expression queries and extra spatial information to further interpret the scRNA-seq data.
|
RRID |
|
|
Software Type |
data preprocessing software, data registration, visualization |
|
Modality |
Gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Mengdi Wang, Liangchen Zhuo, Wenji Ma, Yan Zhuo, Xiaoqun Wang |
|
Year Released |
2022 |
BRain area Input Output (BRIO)
BRIO is a MATLAB-based analysis and visualization tool based on the Allen Brain Atlas connectivity database. It produces custom and user-friendly visualizations and figures for input-output strength of a specific brain area.
|
RRID |
|
|
Software Type |
visualization tool, data analysis tool |
|
Modality |
brain region connectivity |
|
Allen Resource Utilized |
Allen Mouse Brain Connectivity Atlas |
|
Year Released |
2020 |
Brain Observatory Toolbox
The Brain Observatory provides a uniform process and interface to access, navigate, and analyze visual coding neural datasets from the Allen Brain Observatory.
|
Software Type |
data analysis, visualization tool |
|
Allen Resource Utilized |
Allen Brain Observatory |
|
Author |
Ethan Meyers |
|
Year Released |
2021 |
BrainGeneExpressionAnalysis (BGEA)
This MATLAB toolbox can be used to study the whole range of co-expression values between gene pairs, use the Allen Mouse Brain Atlas as a probabilistic resource to estimate the distribution of co-expression networks and compare the expression patterns of highly coexpressed sets of genes to classical neuroanatomy.
|
RRID |
|
|
Software Type |
visualization tool, data analysis software |
|
Modality |
Gene expression, neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Pascal Frange, Michael Hawrylycz, Partha P. Mitra |
|
Year Released |
2013 |
BrainGlobe Atlas API: bg-atlasapi
The bg-atlasapi tool provides a consistent way to process brain atlas data from various sources. It is a common interface for programmers to download and process brain atlas data from multiple sources.
|
RRID |
|
|
Software Type |
data integration, visualization tool |
|
Modality |
general brain atlas data |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Human Brain Atlas |
|
Author |
Luigi Petrucco, Federico Claudi, Adam Tyson, |
|
Year Released |
2020 |
BrainModules
BrainModules is an online interactive visualization tool of brain architecture. There are four modes of visualization: surface, flat, coronal, and sagittal.
|
RRID |
|
|
Software Type |
visualization tool |
|
Modality |
brain region connectivity |
|
Allen Resource Utilized |
Allen Mouse Brain Connectivity Atlas |
|
Author |
Riichiro Hira, Anji Hira, Spencer Smith |
|
Year Released |
2019 |
BrainRender
BrainRender is a generic, open-source Python package for simultaneous and interactive visualization of multidimensional datasets registered to brain atlases. It can render different data types in the same visualization, including user-generated data, and enables using different brain atlases using the same code base. In addition, BrainRender generates high-quality visualizations that can be used interactively and exported as high-resolution figures and animated videos.
|
RRID |
|
|
Software Type |
visualization tool |
|
Modality |
neuroanatomy, morphology |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
F. Claudi, A.L. Tyson, L. Petrucco, T.W. Margrie, R. Portugues, T. Branco |
|
Year Released |
2023 |
CellLocator
Cell Locator is an analysis tool that facilitates manual alignment of tissue samples to common annotated 3D spaces. The user chooses a reference atlas of interest to then create and edit annotation files, and update the slice viewer plane orientation, thus localizing cell and tissue data in a consistent spatial framework.
|
RRID |
|
|
Software Type |
data analysis, data annotation, visualization tool |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Common Coordinate Framework, Allen Human Reference Atlas |
|
Author |
Jean-Christophe Fillion-Robin, David Allemang, Johan Andruejol |
|
Year Released |
2019 |
Cellxgene
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 |
Cocoframer
This R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF-aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer.
|
RRID |
|
|
Software Type |
data analysis software, visualization tool |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Common Coordinate Framework |
|
Author |
Lucas Graybuck |
|
Year Released |
2020 |
Custom Brain Heatmaps Ontop of the Allen Brain Atlas
This page can generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing a google spreadsheet template with specific brain region and gene information.
|
RRID |
|
|
Software Type |
visualization tool, data analysis software |
|
Modality |
Gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas, Human Brain Reference Atlas |
|
Author |
Lior Kirsch |
CutNII
CutNII provides visualization and slicing of 3D isotropic image data as well as various atlases. Through orthogonal views of the three standard planes (coronal, sagittal, horizontal) and a custom-angle slice cut through the volume, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles. Custom slicing then allows for the inspection of anatomical features from non-conventional angles.
|
RRID |
|
|
Software Type |
visualization software |
|
Modality |
histology |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Gergely Csucs |
|
Year Released |
2016 |
Cytosplore Viewer
Cytosplore Viewer is an interactive visual analysis tool that allows for an interactive exploration of hierarchies of cell types. One can visualize transcriptome-wide gene expression in combination with metadata of individual cells, perform differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout the cellular hierarchy, and more.
|
RRID |
|
|
Software Type |
visualization tool |
|
Modality |
cell types |
|
Allen Resource Utilized |
Allen Cell Types Database |
|
Author |
Leiden Computational Biology Center |
|
Year Released |
2018 |
Genomic-and-High-Clustering-Data
The Genomic-and-High-Clustering Data tool analyzes the single-cell RNA-seq dataset from the Allen Mouse Brain Atlas to isolate the analysis of the hierarchical structure and the discovery of important genes in the mouse neocortex.
|
RRID |
|
|
Software Type |
visualization and clustering tool |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Willianto Asalim |
|
Year Released |
2022 |
HERBS: Histological E-data Registration in Brain Space
HERBS facilitates the process of brain atlas image registration and image visualization through two- and three-dimensional visualization of brain atlas volume data, arbitrary slicing, and user-defined data.
|
RRID |
|
|
Software Type |
image registration, image visualization |
|
Modality |
neuroanatomy, histology |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
|
|
Year Released |
2022 |
MeshView
MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, including the Allen Mouse Brain Reference Atlas.
|
RRID |
|
|
Software Type |
visualization software |
|
Modality |
image analysis |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Maja Amedjkouh Puchades, Gergely Csucs, Harry Carey |
|
Year Released |
2019 |
MouseLight
This software generates datasets of whole mouse brain images at submicron resolution which allows reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.
|
RRID |
|
|
Software Type |
visualization tool |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas, Allen Mouse Brain Common Coordinate Framework |
|
Author |
Jayaram Chandrashekar, Michael Economo |
|
Year Released |
2017 |
NeuroInfo
NeuroInfo performs automated brain-wide characterization of cell populations and biochemical marker expression and generates quantitative analysis reports on these objects within individual brain regions. Brain volumes are registered to either the Allen Mouse Brain Atlas or the Waxholm Rat Atlas so that experimental measurements can be accumulated or compared in a standardized coordinate system across animals, cohorts, and laboratories.
| RRID | |
|
Software Type |
visualization tool |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
Neuropixels Trajectory Explorer
The Neuropixels trajectory explorer allows a user to use one or more virtual Neuropixels probes to plan trajectories to target brain regions. This software can be run from MATLAB, but a standalone software version is also included in the GitHub package.
|
Software Type |
visualization tool, data analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Common Coordinate Framework |
|
Author |
Andy Peters |
|
Year Released |
2022 |
Scalable Brain Atlas
The Scalable Brain Atlas provides a unified anatomical and analytic representation of over twenty brain atlases across six species. This tool outputs brain region related data including anatomical connectivity, 3d reconstructions, and coordinate transformations.
|
RRID |
|
|
Software Type |
visualization tool, data analysis |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Reference Atlas, Allen Mouse Common Coordinate Framework, Allen Mouse Brain Atlas |
|
Author |
Rembrandt Bakker, Paul Tiesinga, Rolf Kötter |
|
Year Released |
2015 |
Single Cell Portal
The Single Cell Portal (SCP) is both a data hub and a cell visualization tool. The user can search by study or 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 |
STEB (Spatiotemporal Pattern Exploration of Brain)
STEB (Spatiotemporal Pattern Exploration of Brain) is a web-based visual analytics tool for the developing mouse brain. It provides comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns. The tool is designed in JavaScript and D3.js.
|
RRID |
|
|
Software Type |
visualization, visual analysis |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Developing Mouse Brain Atlas |
|
Year Released |
2016 |
VisiGene Image Browser
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 |
VoxHunt
VoxHunt systematically compares single-cell transcriptomes to three-dimensional in situ hybridization (ISH) data in order to analyze brain organoid patterning, developmental state, and cell composition.
|
RRID |
|
|
Software Type |
visualization tool, annotation tool |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Developing Mouse Brain Atlas, Developing Human Brain Atlas |
|
Author |
Jonas Simon Fleck |
|
Year Released |
2023 |
UCSC Cell Browser
The USCS Cell Browser is a 2-dimensional cell viewer which displays cells as a dimensionality reduction plot with gene expression (single-cell RNA sequencing) data overlaid.
|
RRID |
|
|
Software Type |
visualization tool, data analysis |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Cell Types Database |
|
Author |
Max Haeussler, Matthew L Speir, Aparna Bhaduri, Nikolay S Markov, Pablo Moreno, et al. |
|
Year Released |
2021 |
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.
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