Data Preprocessing, Registration, and Integration Tools

Abagen 

Link 

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. 

RRID	SCR_023832
Software Type	data processing software
Modality	gene expression
Allen Resource Utilized	Allen Human Brain Atlas
Author	Ross Markello
Year Released	2021

ABBA: Aligning Big Brains & Atlases

Link 

ABBA is a Fiji plugin that facilitates 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.

RRID	SCR_023857
Software Type	data registration
Modality	neuroanatomy
Allen Resource Utilized	Allen Mouse Common Coordinate Framework
Author	Nicolas Chiaruttini
Year Released	2023

ABI-expression-data-generator 

Link 

ABI-expression-data-generator is 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. 

RRID	SCR_023834
Software Type	data processing software, data registration
Modality	gene expression
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Horea Christian
Year Released	2020

Allen Density Vectors

Link 

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. 

RRID	SCR_023841
Software Type	data navigation software
Modality	neuroanatomy
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Blue Brain Project
Year Released	2023

AllenDigger

Link Relevant Publication

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	SCR_023812
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

AP-histology

Link 

AP-histology is a data pipeline that aligns histology images to the Allen Common Coordinate Framework.

RRID	SCR_023847
Software Type	data registration
Modality	histology
Allen Resource Utilized	Allen Common Coordinate Framework
Author	Andy Peters
Year Released	2023

Atlas Densities

Link 

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 of the mouse brain volume. 

RRID	SCR_023839
Software Type	data integration software
Modality	mouse cell types
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Blue Brain Project
Year Released	2023

AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures 

Link Relevant Publication

The Atlas Ontology Model (AOM) 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 and will accelerate neuroscience data integration. 

RRID	SCR_023813
Software Type	educational, data integration tool
Modality	ontology
Allen Resource Utilized	Allen Mouse Brain Atlas, Allen Common Coordinate Framework
Author	Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Time Dickscheid, Jan G. Bjaalie, et al.
Year Released	2011

BrainGlobe Atlas API: bg-atlasapi

Link 

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	SCR_023848
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, David Stansby
Year Released	2020

Brainmapr

Link Relevant Publication 

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	SCR_023816
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 

Link 

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 that is compatible with multiple atlases and species. 

RRID	SCR_023858
Software Type	data registration
Modality	brain imaging
Allen Resource Utilized	Allen Mouse Brain Reference Atlas, Allen Human Brain Atlas
Author	Adam Tyson, Charly Rousseau
Year Released	2020

BrainRegionMarkers

Link 

BrainRegion markers is an R package that 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. 

RRID	SCR_023836
Software Type	data preprocessing software
Modality	genetics
Allen Resource Utilized	Allen Human Brain Atlas

DeepSlice

Link Relevant Publication

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 cut sections and is best for brightfield images.

RRID	SCR_023854
Software Type	data registration
Modality	histology, imaging
Allen Resource Utilized	Allen Mouse Brain Atlas, Common Coordinate Framework
Author	Harry Carey, Michael Pegios
Year Released	2023

HERBS: Histological E-data Registration in Brain Space

Link 

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	SCR_022776
Software Type	image registration, image visualization
Modality	neuroanatomy, histology
Allen Resource Utilized	Allen Mouse Brain Atlas
Author	Jingyi G. Fuglstad
Year Released	2022

JuGEx

Link Relevant Publication 

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 gene expression, brain structure, and function knowledge.

RRID	SCR_023838
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

MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis 

Link 

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 Human Brain Atlas in order to create a comprehensive, integrated data platform. 

RRID	SCR_023822
Software Type	data integration
Modality	gene expression
Allen Resource Utilized	Allen Human Brain Atlas
Author	Gaia Rizzo, Mattia Veronese, Paul Expert
Year Released	2016

MIRACL

Link 

MIRACL is an automated software resource that 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. This tool serves as an open-source pipeline for automated registration of mice clarity data to the Allen Mouse Brain Reference Atlas.

RRID	SCR_020945
Software Type	data registration
Modality	histology, image registration
Allen Resource Utilized	Allen Mouse Brain Reference Atlas, Allen Mouse Connectivity Atlas
Author	Magen Goubran
Year Released	2023

MorphAPI

Link 

MorphAPI is a Python package to facilitate downloading neuronal morphological reconstructions from publicly available datasets. With the provided APIs, the user can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization. 

RRID	SCR_023851
Software Type	data registration
Modality	morphology
Allen Resource Utilized	Allen Cell Types Database
Author	Federico Claudi
Year Released	2022

Nutil

Link 

Nutil is a data processing resource that 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, requiring no prior software experience. 

RRID	SCR_017183
Software Type	data processing software
Modality	spatial analysis, histology
Allen Resource Utilized	Allen Mouse Brain reference atlas
Author	Sharon Yates, Nicolaas Groeneboom
Year Released	2019

QuickNII

Link 

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. 

RRID	SCR_016854
Software Type	data registration
Modality	image analysis
Allen Resource Utilized	Allen Mouse Brain Reference Atlas, Common Coordinate Framework
Author	Maja Amedjkouh Puchades, Gergely Csucs, Sharon Yates
Year Released	2018

Process Genes List

Link Relevant Publication 

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	SCR_023823
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

SHARCQ

Link

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 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 Reference Atlas.

RRID	SCR_022498
Software Type	data registration, data analysis
Modality	cell type, histology
Allen Resource Utilized	Allen Mouse Brain Reference Atlas
Author	Kris Lauridsen, Annie Ly
Year Released	2022

SMART: Semi-manual alignment to reference templates

Link Relevant Publication

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	SCR_019265
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

VisuAlign

Link 

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	SCR_017978
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.