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https://github.com/UCI-CARL/ABADV

Web based gene expression energy visualization tool.Created for visualizing expression energy data from the Allen Brain Atlas.ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures.

Proper citation: Allen Brain Atlas-Driven Visualizations (RRID:SCR_023811) Copy   

•   Source: SciCrunch Registry

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

Software tools to split brain atlas regions and refine annotations accordingly. Applicable to the Allen Mouse Brain Atlas

Proper citation: Atlas Splitter (RRID:SCR_023842) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-direction-vectors

Software tools to compute direction vectors in context of brain atlases.

Proper citation: Atlas Direction Vectors (RRID:SCR_023841) Copy   

•   Source: SciCrunch Registry

https://github.com/itsasimiqbal/SeBRe

Software high-throughput Mask R-CNN based toolbox to generate brain atlas through deep learning. Used for segmenting brain regions of interest.

Proper citation: Segmenting Brain Regions (RRID:SCR_023849) Copy   

•   Source: SciCrunch Registry

http://ibislab.ce.unipr.it/software/hippo/

Software pipeline aiming at detecting transcripts enriched in hippocampal neuropil of adult mice, by systematically exploring high resolution images contained in Mouse Brain Atlas. Data mining tool that can provide information to select target genes whose nature will be studies and confirmed using biological tests.

Proper citation: Hippo-ATESC (RRID:SCR_023809) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/view/brain-mapping

Software tool to map histological slice sequences to Allen Mouse Brain Atlas without 3D Reconstruction. Automatically maps histological slice to its corresponding plane in Allen Mouse Brain Atlas to build plane wise mapping and then perform 2D nonrigid registration to build pixel wise mapping.

Proper citation: brain-mapping (RRID:SCR_023845) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaoqunwang-lab/Allendigger

Software tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Allen Brain Atlas. Software toolkit to collect and preprocess expression data from Allen Brain Atlas and allow query to visualize spatial distribution of genes of interest, characterize spatial heterogeneity of brain, and register cells from single-cell transcriptomics data to fine anatomical brain regions via machine learning methods with high accuracy.

Proper citation: AllenDigger (RRID:SCR_023812) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/atlasplot

Software package to simplify process of producing graphics for expression data available in the Allen Institute's Brain Atlases. Related to Allen Mouse Brain Atlas.

Proper citation: Atlasplot (RRID:SCR_023810) Copy   

•   Source: SciCrunch Registry

https://github.com/alleninstitute/cocoframer

Software 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.

Proper citation: Cocoframer (RRID:SCR_023817) Copy   

•   Source: SciCrunch Registry

https://github.com/asalimw/Genomic-and-High-Dimensional-Data

Software tool analyzes 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.

Proper citation: Genomic-and-High-Dimensional-Data (RRID:SCR_023828) 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/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://github.com/PolarBean/DeepSlice?

Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

Proper citation: DeepSlice (RRID:SCR_023854) Copy   

•   Source: SciCrunch Registry

http://mouse.brainarchitecture.org/cell-type-analysis-toolbox

Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.

Proper citation: Cell Type Analysis Toolbox (RRID:SCR_023852) Copy   

•   Source: SciCrunch Registry

https://github.com/IBT-FMI/ABI-expression-data_generator

Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas.

Proper citation: ABI-expression-data-generator (RRID:SCR_023834) 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://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

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

https://github.com/Aswendt-Lab/AIDAhisto

Software atlas based imaging data analysis tool for quantitative mouse brain histology. Can automatically detect cells in histological mouse brain and spinal cord sections of interest.

Proper citation: AIDAhisto (RRID:SCR_023818) Copy   

•   Source: SciCrunch Registry