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https://github.com/petersaj/AP_histology

Software data pipeline which aligns histology images to the Allen CCF.

Proper citation: AP-histology (RRID:SCR_023847) Copy   

•   Source: SciCrunch Registry

https://github.com/SainsburyWellcomeCentre/ara_tools

Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. 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.

Proper citation: ARA Tools (RRID:SCR_023826) Copy   

•   Source: SciCrunch Registry

https://github.com/GuillermoPoblete/PGL

Software R package which links genetics and human brain imaging by using genes associated with disease and calculating 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 csv with the results.

Proper citation: Process Genes List (RRID:SCR_023823) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/spm_mouse_toolb#

Software 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.

Proper citation: PET-CT mouse brain toolbox (RRID:SCR_023821) Copy   

•   Source: SciCrunch Registry

https://singlecell.broadinstitute.org/single_cell

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

Proper citation: Single Cell Portal (RRID:SCR_014816) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-4/search?q=*

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).

Proper citation: Integrated Brain Gene Expression (RRID:SCR_004197) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/bg-atlasapi

Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources.

Proper citation: BrainGlobe Atlas API (RRID:SCR_023848) Copy   

•   Source: SciCrunch Registry

http://liorkirsch.github.io/brain-heatmap-web/

Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.

Proper citation: Brain heatmap (RRID:SCR_023815) Copy   

•   Source: SciCrunch Registry

http://fair.dei.unipd.it/software/

Software platform for 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 in order to create comprehensive, integrated data platform.

Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

•   Source: SciCrunch Registry

https://www.microns-explorer.org/

Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons.

Proper citation: Microns Explorer (RRID:SCR_021678) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/cran/WGCNA/man/BrainRegionMarkers.html

Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.

Proper citation: BrainRegionMarkers (RRID:SCR_023836) Copy   

•   Source: SciCrunch Registry

https://github.com/benfulcher/GCEA_FalsePositives

Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.

Proper citation: GCEA_FalsePositives (RRID:SCR_023835) Copy   

•   Source: SciCrunch Registry

https://github.com/LeonDLotter/ABAnnotate/tree/v0.1.0

Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.

Proper citation: ABAnnotate (RRID:SCR_023833) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-densities

Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume.

Proper citation: Atlas Densities (RRID:SCR_023839) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-alignment-meter

Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file.

Proper citation: Atlas Alignment Meter (RRID:SCR_023843) Copy   

•   Source: SciCrunch Registry

https://cells.ucsc.edu/

Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.

Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy   

•   Source: SciCrunch Registry

https://quint-workflow.readthedocs.io/en/latest/QUINTintro.html

Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.

Proper citation: QUINT (RRID:SCR_023856) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry