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Community Tools

In addition to the open resources developed by The Allen Institute for Brain Science, many external institutions, universities, and individuals have created computational or educational tools which utilize Allen Brain Map data. This database centralizes the location of these tools to further our mission of open science.

If you know of a tool that you believe satisfies the criteria for this database, please fill out this form to submit your tool. For all other feedback, use our contact form.

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.

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Visualization
BICAN Basal Ganglia Epigenome Browser

The Basal Ganglia Epigenome Browser is an interactive web-based platform integrating multi-omics and cross-species basal ganglia single-cell/epigenomic data.

Data Analysis
Brain Street View

Load and plot Allen Connectivity Data in MATLAB

Visualization
Neuron SWC editor

The free online editor lets users visualize, edit, import, and export neuron SWC files in 2D/3D and save transparent PNGs. The files can be used in simulation software like Neuron.

Processing, Registration, Integration
BREIN (Brain Region Expression Intensity Neuroanalysis)

BREIN can be used to analyzes RNA in-situ hybridization or immunohistochemical images. It can register images to Allen reference atlas and calculates the signal intensity per brain region, and outputs a spreadsheet of the results.

Data Analysis
ElecFeX (Electrophysiological Feature eXtraction)

ElecFeX is a MATLAB-based toolbox for extracting electrical features from current-clamp recordings. It has a graphical user interface enabling an effortless batch analysis for electrophysiologists. Supported data formats include ABF, IBW, DAT, and NWB.

Data Repositories
Recombinase (cre) Activity

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

Data Repositories
NIAGADS

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

Visualization
NeuronBench

NeuronBench is a web platform allowing users to interact with biologically realistic model neurons in the browser, and allows educators and researchers to develop these models with fast visual feedback.

Data Repositories
BIL (Brain Image Library)

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 strucure.

Educational
Learning How to Code While Analyzing an Open Access Electrophysiology Dataset

This resource is a lesson plan for users to begin coding in Python and interact with and analyze electrophysiology data from the Allen Institute for Brain Science.

Educational
QUINT

The QUINT workflow includes a suite of various software to form an analysis pipeline of atlas-based quantification of labeled features in histological images from a mouse or rat brain.

Data Repositories
Gene Expression Omnibus (GEO)

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

Data Repositories
Open Source Brain

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.

Data Repositories
NeuroMorpho

NeuroMorpho is a curated inventory of digitally reconstructed neurons along with peer-reviewed publications, focusing on some of the most complete axonal arborizations digitally available in the community.

Data Repositories
SageBionetworks Portals

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

Data Repositories
DANDI (Distributed Archives for Neurophysiology Data Integration)

DANDI is a platform for publishing, sharing, and processing neurophysiology data. It is a living repository that enables collaboration within and across labs, and contains neurophysiology data including electrophysiology, optophysiology, and more.

Visualization
5-HT2A MERFISH

Custom visualizer for MERFISH dataset provided by [Yao et al., 2023] By Roberto De Filippo

Data Repositories
ModelDB

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.

Educational
A Course-based Research Experience Using Allen Brain Map

This resource mimics a course for users to utilize Allen Brain Map resources to develop a research question, document their methodology and results, and eventually present their work in a conference environment.

Data Repositories
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas

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. ...

Data Repositories
dbGaP

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 genotype and phenotype in humans.

Processing, Registration, Integration
MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis

MENGA is a platform for the integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas.

Data Analysis
Allen Density Vectors

AllenDensityVectors contains the commands to establish direction vectors (3d unit vectors associated to voxels of a brain region) for the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.

Processing, Registration, Integration
Nutil

Nutil is a data processing resource which simplifies and streamlines the pre-and-post processing of 2D brain image data from both the mouse and rat. To use Nutil, the user specifies the input and output parameters in the GUI.

Processing, Registration, Integration
Atlas Densities

AtlasDenities contains the tools to create the BBP Cell Atlas, using the Allen Mouse Brain Atlas and collected literature density values. It provides a list of volumetric files that provides cell type density estimates for each voxel.

Educational
Atlas Ontology Model (AtOM)

The Atlas Ontology Model (AtOM) identifies and defines the relationships between four common atlases and characterizes their properties and organization. This model can serve as a suggestion for minimum requirements for atlases.

Annotation & Segmentation
Atlas Alignment Meter

The Atlas Alignment Meter is a tool based in Python which can measure the slice-to-slice jaggedness of a volumetric dataset, only in the form of an NRRD file.

Data Repositories
NeMO: Neuroscience Multi-omic Data Archive

A data repository specifically focused on the storage and dissemination of omic data generated from the BRAIN Initiative, SCORCH consortium and other brain research projects.

Annotation & Segmentation
Atlas Splitter

The Atlas Splitter contains tools to split brain atlas regions and refine annotations accordingly, applicable to the Allen Mouse Brain Atlas.

Processing, Registration, Integration
Abagen

This package provides a Python interface for acquiring and analyzing the Allen Human Brain Atlas microarray expression data. It includes a reproducible workflow for processing the microarray expression data for further analysis.

Processing, Registration, Integration
ABI-expression-data-generator

A package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas. It queries the database, can download available data, convert it from a raw format to NIfTI, and register it to a standard space.

Annotation & Segmentation
SeBRe-Segmenting Brain Regions

SeBRe is a fully automated method for segmenting brain regions of interest. This is a Mask R-CNN-based toolbox created through deep learning.

Data Repositories
Blue Brain Cell Atlas

The Blue Brain Cell Atlas describes number, types, and positions of cells in all areas of mouse brain. It provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and more.

Processing, Registration, Integration
Integrated Brain Gene Expression

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

Data Repositories
Brain Architecture Project

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 brainwide mesoscopic connectivity diagram.

Processing, Registration, Integration
QuickNII

QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images to 3D atlas reference space, facilitating data integration with the Allen Mouse Brain Reference Atlas.

Processing, Registration, Integration
MIRACL

An automated software resource which collates histologically cleared volumes alongside connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.

Processing, Registration, Integration
Brainreg

Brainreg is a Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image. This is an automated registration process which is compatible with multiple atlases and species.

Processing, Registration, Integration
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.

Processing, Registration, Integration
DeepSlice

DeepSlice is an automated data registration tool based in Python which aligns mouse histology with the Allen Mouse Common Coordinate Framework. This tool only works on coronally cute sections and is best for brightfield images.

Processing, Registration, Integration
ABBA (Aligning Big Brains & Atlases)

ABBA is a Fiji plugin which allows for registering thin serial sections (coronal, sagittal, horizontal) to several atlases. The compatible atlases include Allen Mouse Common Coordinate Framework, the Waxholm Rat Brain Atlas, and all BrainGlobe atlases.

Visualization
CutNII

Visualization and slicing of 3D isotropic image data as well as various atlases, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles.

Visualization
BrainModules

BrainModules is an online interactive visualization tool of brain architecture. There are four modes of visualization: surfarce, flat, coronal, and saggital.

Processing, Registration, Integration
BrainRegionMarkers

BrainRegion markers is an R package which provides a matrix of a predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.

Data Repositories
VisiGene Image Browser

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.

Processing, Registration, Integration
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.

Visualization
BrainRender

BrainRender is a generic, open-source Python package for simultaneous and interactive visualization of multidimensional datasets registered to brain atlases. It can easily render different data types in the same visualization.

Processing, Registration, Integration
MorphAPI

A Python package to facilitate downloading neuronal morphological reconstructions from publicly available datasets. User can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization.

Visualization
VoxHunt

VoxHunt systematically compares single cell transcriptomes to three-dimensional in situ hybridization(ISH) data to analyze brain organoid patterning, developmental state, and cell composition.

Processing, Registration, Integration
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 with high accuracy.

Processing, Registration, Integration
AP_histology

AP-histology is a data pipeline which aligns histology images to the Allen CCF.

Data Analysis
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.

Data Repositories
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, and more.

Visualization
Allen Brain Atlas-Driven Visualizations

ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures. It utilizes Data-Driven Documents (D3) to drive the creation and control of visualizations in web browsers.

Data Analysis
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.

Processing, Registration, Integration
SMART: Semi-manual alignment to reference templates

SMART is an R package which 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.

Visualization
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.

Annotation & Segmentation
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.

Visualization
MouseLight

This software generates datasets of whole mouse brains imaged at submicron resolution that allows reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.

Visualization
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.

Data Analysis
ABAT (Allen Brain Atlas Tools)

ABAT (Allen Brain Atlas Tools) stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from the Allen Brain Atlas.

Visualization
Cytosplore Viewer

Cytosplore Viewer is an interactive visual analysis tool which allows for an interactive exploration of hierarchies of cell types. One can visualize transcriptome-wide gene expression in combination with metadata of individual cells and more.

Data Repositories
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.

Visualization
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.

Visualization
Scalable Brain Atlas

A unified anatomical and analytic representation of over twenty brain atlas across six species. This tool outputs brain region related data including anatomical connectivity, 3d reconstructions, and coordinate transformations.

Visualization
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 packa...

Data Analysis
CellLocator

Cell Locator is an analysis tool which facilitates manual alignment of tissue samples to common annotated 3D spaces. The user chooses a reference atlas of interest and can then create and edit annotation files, and more.

Visualization
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 more.

Visualization
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 hierarchical structure and the discovery of important genes in the mouse neocortex.

Data Analysis
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.

Data Analysis
MeshGen

MeshGen generates separate mesh files for each label present in the segmentation volume, simplifying the creations of procedural meshes.

Data Analysis
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.

Processing, Registration, Integration
GCEA False Positives Toolbox

A solution for gene-category enrichment analysis (GCEA). It shows that within-category gene-gene coexpression and spatial autocorrelation are key drivers of the false-positive bias.

Data Repositories
BrainStars

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

Visualization
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.

Data Analysis
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.

Data Analysis
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.

Processing, Registration, Integration
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.

Processing, Registration, Integration
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 ROI size.

Processing, Registration, Integration
Allen Mouse Brain ImageLoader

The Allen Mouse Brian 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 sagittal, 528 coronal and 320 axial).

Visualization
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.

Data Analysis
ABAnnotate

ABAnnotate is a Matlab-based toolbox which 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.

Data Analysis
Mouse_abi_tool

The mouse-abi-tool is a data anaysis tool used to pull gene expression data from the Allen Institute API in Common Coordinate Framework v2 space.

Data Analysis
VisuAlign

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.

Data Analysis
GOI2ROI

This Python package utilizes spatial, anatomical, 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).

Data Analysis
NS-Forest

NS-Forest is a software tool which takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. It utilizes random forest of decision trees machine learning approach.

Data Analysis
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.

Data Analysis
Atlasplot

This R package creates simple reproducible plots for data analysis purposes. This package aims to simplify the process of producing graphics for the expression data available in the Allen Institute's Brain Atlases.

Data Analysis
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.

Processing, Registration, Integration
SHARCQ

SHARCQ is a group of software tools which register histological section images and cell count locations to a mouse brain atlas. It features semi automated workflow and GUI for automated brain slice histology alignment, registration, and more.

Data Analysis
The 3D Brain Atlas 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 models.

Data Repositories
Linked Neuron Data

Linked Neuron Data provides multiple interactive resources for extracting, integrating, linking, and analyzing brain data and knowledge from multiple scale and multiple data sources.

Data Analysis
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.

Data Analysis
Brainmapr

Brainmapr is an R package to infer 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.

Processing, Registration, Integration
Process Genes List

ProcessGeneLists (PGL) is an R package which 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.

Visualization
Custom Brain Heatmaps Ontop of the Allen Brain Atlas

This page can generate brain heatmaps for the human or mouse brain on top of the Allen Brain Atlas by editing a google spreadsheet template with specific brain region and gene information.

Data Analysis
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.

More Support Resources

Tutorials & How-Tos
Walk throughs for how to use our resources and apply them to your work
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Documentation
Detailed references for how data was generated and how the tools can be used
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Citing Our Sources
Guidance on how to cite our resources when you use them in your work
Policy
Educator Resources
Support for teaching students with the Allen Brain Map
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