Data Analysis Tools
Data Analysis 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 |
|
Year Released |
2012 |
ABAEnrichment
ABAEnrichment is an R package that tests for expression enrichment in specific brain regions at different developmental stages, using expression information gathered from multiple regions of the adult and developing human brain together with ontologically organized structural information about the brain.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Human Brain Atlas, Allen Developing Human Brain Atlas, Brain Explorer |
|
Author |
Steffi Grote, Kay Prufer, Janet Lelso, Michael Dannemann |
|
Year Released |
2016 |
ABAnnotate
ABAnnotate is a Matlab-based toolbox that performs ensemble-based gene-category enrichment analysis (GCEA) on volumetric human neuroimaging data via brain-wide gene expression patterns derived from the Allen Human Brain Atlas. It utilizes a nonparametric method using spatial autocorrelation-corrected phenotype null maps for the estimation of gene-category null ensembles.
|
RRID |
|
|
Software Type |
data analysis software, data annotation tool |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Leon Lotter |
| Year Released | 2022 |
ABAT: Allen Brain Atlas Tools
ABAT (Allen Brain Atlas Tools) stores multiple MATLAB functions to read, analyze, and visualize various kinds of data from the Allen Human Brain Atlas.
|
RRID |
|
|
Software Type |
data analysis |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Zonglei Zhen |
|
Year Released |
2017 |
AIDAhisto
AIDAhisto is an imaging data analysis tool for quantitative mouse brain histology based on brain atlases. It can automatically detect cells in histological mouse brain and spinal cord sections of interest.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
histology |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Spinal Cord Atlas |
|
Author |
Niklas Pallast, Leon Scharwächter, Markus Aswendt |
|
Year Released |
2019 |
Allen CCF Tool
The Allen CCF tool provides MATLAB code to work with the Allen Mouse Brain CCF data, specifically the 10µm voxel 2017 version.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Common Coordinate Framework |
|
Author |
Philip Shamash, Andy Peters, etc |
|
Year Released |
2022 |
Allen Mouse Brain Image Loader
The Allen Mouse Brain Image Loader contains two small tools which render the annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 saggital, 528 coronal, and 320 axial).
|
RRID |
|
|
Software Type |
image analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Torben Dohrn |
|
Year Released |
2016 |
Alleninf
Alleninf is a method to test hypotheses about the relation of patterns found in statistical maps with gene expression measured in postmortem brains. This software also refines the corregistration coordinates provided by the Allen Institute.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Krzysztof J Gorgolewski, Andrew S Fox, Luke Chang, Alexander Schäfer, Katrin Arélin |
|
Year Released |
2018 |
ARA Tools
ARA Tools is a collection of MATLAB functions to analyze mouse whole-brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Rob Campbell, Antonin Blot, Steven J. West, Adam Tyson |
|
Year Released |
2022 |
Atlasplot
This R package creates simple reproducible plots for the Allen Institute's brain atlases. This package aims to simplify the process of producing graphics for the expression data available in the Allen Institute's Brain Atlases. Additionally, it will be coupled with individual data packages, allowing anyone to easily access this data resource.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Jeremy Miller, Charlie Edelson |
|
Year Released |
2021 |
Azimuth
This web application uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. This 'reference-based mapping' pipeline inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery).
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Year Released |
2023 |
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 the 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 |
Brainmapr
Brainmapr is an R package to infer the spatial location of neural progenitor subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas.
|
RRID |
|
|
Software Type |
data analysis software, data integration |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Developing Mouse Brain Atlas |
|
Author |
Jean Fan- Kharchenko Lab at Biomedical Informatics (HMS) |
|
Year Released |
2015 |
Brainreg-segment
The brainreg-segment tool works alongside the brainreg tool, allowing for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first.
|
RRID |
|
|
Software Type |
data segmentation, data analysis |
|
Modality |
brain imaging |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Human Brain Atlas |
|
Author |
Adam Tyson, Charlie Rosseau |
|
Year Released |
2023 |
CellLocator
Cell Locator is an analysis tool that facilitates the 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 |
Cell Type Analysis Toolbox
The Cell Type Analysis Toolbox is a cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.
|
RRID |
|
|
Software Type |
data analysis |
|
Modality |
cell types |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Yongsoo Kim, Guangyu Robert Yang, Kith Pradhan, Kannan Umadevi Venkataraju, Mihail Bota, et al. |
|
Year Released |
2017 |
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 |
|
Year Released |
2016 |
Genomic-and-High-Dimensional-Data
The Genomic-and-High-Dimensional 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 |
GCEA False Positives Toolbox
This software toolbox makes a solution for gene-category enrichment analysis (GCEA) false positives available. It shows that within-category gene-gene coexpression and spatial autocorrelation are critical drivers of the false-positive bias and this toolbox contains flexible ensemble-based null models that can account for these effects.
|
RRID |
|
|
Software Type |
data processing software, data analysis software |
|
Modality |
gene expression, structural connectivity |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Human Brain Atlas |
|
Author |
Ben Fulcher |
|
Year Released |
2021 |
GOI2ROI
This Python package utilizes spatial, anatomical, and microarray expression data from the Allen Institute for Brain Science. This program maps genes of interest (Goi) by their levels of expression to brain regions (Roi). The identified regions that co-express the input Goi can, in turn, be studied further with many experimental modalities. This program can be customized to map gene expression data and identify significant Roi from similar reference expression data in other contexts outside of neuroscience.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression, neuroanatomy |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Macarena Aloi |
|
Year Released |
2022 |
Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing)
Hippo-ATESC is an automatic pipeline aiming at detecting transcripts enriched in the hippocampal neuropil of adult mice by systematically exploring the high resolution images contained in the Mouse Brain Atlas. This is a data mining tool that can provide helpful information to select target genes whose nature will be studied and confirmed using biological tests.
|
RRID |
|
|
Software Type |
data mining |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Roberto Ugolotti, Pablo Mesejo, Samantha Zongaro, Barbara Bardoni, Gaia Berto, et al. |
|
Year Released |
2013 |
JuGEx
JuGEx combines data from the Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.
|
RRID |
|
|
Software Type |
data integration software, data analysis software |
|
Modality |
genetics |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Sebastian Bludau, Thomas W. Mühleisen, Simon B. Eickhoff, Michael J. Hawrylycz, Sven Cichon, et al. |
|
Year Released |
2018 |
Linked Neuron Data
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 |
MeshGen
MeshGen generates separate mesh files for each label present in the segmentation volume, simplifying the creation of procedural meshes.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Common Coordinate Framework, Mouse Brain Atlas |
|
Author |
John Tsiombikas, Gergely Csucs |
|
Year Released |
2016 |
Mouse_abi_tool
The mouse-abi-tool is a data analysis tool used to pull gene expression data from the Allen Institute API in the Common Coordinate Framework v2 space.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
gene expression |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Common Coordinate Framework |
|
Author |
Eli Cornblath |
|
Year Released |
2020 |
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 |
NS-Forest
NS-Forest is a software tool that takes cluster results from single-cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. It utilizes a random forest of decision trees machine learning approach. It is used to determine the minimum set of marker genes whose combined expression identified cells of a given type with maximum classification accuracy.
|
RRID |
|
|
Software Type |
data analysis |
|
Modality |
gene expression, cell type |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Brian Aevermann, Richard Scheuermann |
|
Year Released |
2018 |
Pet-CT Mouse Brain Toolbox
The proposed toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images.
|
RRID |
|
|
Software Type |
image analysis, cell detection |
|
Modality |
neuroimaging |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Luca Presotto, V. Bettinardi, D. Mercatelli, M. Picchio, M. Morari |
|
Year Released |
2022 |
Pinpoint
Pinpoint is a neuropixels trajectory planner for designing multi-probe insertions, utilizing the Allen Mouse Brain Common Coordinate Framework. This is a MATLAB-based program.
|
RRID |
|
|
Software Type |
data analysis software |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Institute Common Coordinate Framework |
|
Author |
Dan Birman, Kenneth Yang, Yoni Browning |
|
Year Released |
2023 |
Process Genes List
ProcessGeneLists (PGL) is an R package that links genetics and human brain imaging by using genes associated with a disease and calculating a normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return a CSV with the results.
|
RRID |
|
|
Software Type |
data integration, data analysis software |
|
Modality |
gene expression, neuroanatomy |
|
Allen Resource Utilized |
Allen Human Brain Atlas |
|
Author |
Guillermo F. Pollete, Savannah N. Gosnell, Matthew Meyer, Mary Fang, Tien Nquyen, Michelle A. Patriquin, David Nielsen, Thomas Kosten, Ramiro Salas |
|
Year Released |
2023 |
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 |
SHARCQ
SHARCQ is a group of software tools that register histological section images and cell count locations to a mouse brain atlas. Semi-automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification make it possible to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and analyze regions of interest data by registering locations of fluorescently labeled cells to standardized regions of the Allen Mouse Brain Atlas.
|
RRID |
|
|
Software Type |
data registration, data analysis |
|
Modality |
cell type, histology |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas |
|
Author |
Kris Lauridsen, Annie Ly |
|
Year Released |
2022 |
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 |
SMART: Semi-manual alignment to reference templates
SMART is an R package that builds a pipeline to process whole brain imaging datasets. This pipeline includes image registration, segmentation, coordinate navigation, standardized organization, and novel methods to parse through whole brain datasets and visualize data across various brain regions.
|
RRID |
|
|
Software Type |
data alignment, data segmentation, data registration, data analysis |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Atlas, Allen Common Coordinate Framework |
|
Author |
Michelle Jin, Joseph Nguyen |
|
Year Released |
2019 |
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 a 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 |
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 |
VisuAlign
VisuAlign is a Java-based software tool for applying user-guided nonlinear refinements (inplane) to existing, affine 2D-to-3D registration. It can be used for precise quantitative analysis of residual anatomical variability among test subjects after registration.
|
RRID |
|
|
Software Type |
data analysis software, data registration |
|
Modality |
neuroanatomy |
|
Allen Resource Utilized |
Allen Mouse Brain Reference Atlas |
|
Author |
Gergely Csucs |
|
Year Released |
2022 |
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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