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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

https://quadbio.github.io/VoxHunt/

Software package for assessing brain organoid patterning, developmental state, and cell composition through systematic comparisons of single cell transcriptomes to three-dimensional in situ hybridization data from the Allen Brain Atlas and number of other useful reference datasets.

Proper citation: VoxHunt (RRID:SCR_023829) 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://biop.github.io/ijp-imagetoatlas/

Software Fiji plugin for registering thin serial sections: coronal, sagittal, horizontal, to compatible atlases including Allen Mouse Common Coordinate Framework, Waxholm Rat Brain Atlas, and all BrainGlobe atlases.

Proper citation: Aligning Big Brains and Atlases (RRID:SCR_023857) Copy   

•   Source: SciCrunch Registry

https://github.com/VirtualBrainLab/Pinpoint

Software electrophysiology tool for planning Neuropixels recordings. Neuropixels trajectory planner for designing multi-probe insertions,utilizing the Allen Mouse Brain Common Coordinate Framework.

Proper citation: Pinpoint (RRID:SCR_023840) 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

http://bioconductor.org/packages/ABAEnrichment//

Software 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, both provided by the Allen Brain Atlas.Used to test for gene set expression enrichment in adult and developing human brain.

Proper citation: ABAEnrichment (RRID:SCR_023814) 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

http://hms-dbmi.github.io/brainmapr/

Software R package to the 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.

Proper citation: Brainmapr (RRID:SCR_023816) Copy   

•   Source: SciCrunch Registry

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

Software provides visualization and slicing of 3D isotropic image data as well as various atlases. Through orthogonal views of three standard planes (coronal, sagittal, horizontal) and custom-angle slice cut through the volume, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles. Custom slicing then allows for the inspection of anatomical features from non-conventional angles.Custom-angle slicer for brain atlas volumes.

Proper citation: CutNII (RRID:SCR_023824) Copy   

•   Source: SciCrunch Registry

https://github.com/macarenasa/goi2roimapping

Software 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). 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.

Proper citation: goi2roimapping (RRID:SCR_023820) Copy   

•   Source: SciCrunch Registry

https://miracl.readthedocs.io/en/latest/

Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.

Proper citation: MIRACL (RRID:SCR_020945) Copy   

•   Source: SciCrunch Registry

https://github.com/wildrootlab/SHARCQ

Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.

Proper citation: SHARCQ (RRID:SCR_022498) Copy   

•   Source: SciCrunch Registry

https://github.com/JCVenterInstitute/NSForest/releases

Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy.

Proper citation: NS-Forest (RRID:SCR_018348) Copy   

•   Source: SciCrunch Registry

https://www.mozak.science/landing

Scientific discovery game about neuroscience that helps to build models of brain cells.

Proper citation: Mozak (RRID:SCR_021008) Copy   

•   Source: SciCrunch Registry

https://sagebionetworks.org/portals/

Platform provides web interfaces for research institutions to exchange, share, and publish curated data and other digital resources.

Proper citation: SageBionetworks Portals (RRID:SCR_023844) Copy   

•   Source: SciCrunch Registry

https://github.com/jtsiomb/meshgen

Software tool to simplify creation of procedural meshes. Used to generate separate mesh files for each label present in segmentation volume, simplifying creations of procedural meshes.

Proper citation: MeshGen (RRID:SCR_023819) Copy   

•   Source: SciCrunch Registry

https://azimuth.hubmapconsortium.org/

Web application that uses annotated reference dataset to automate processing, analysis, and interpretation of new single cell RNA-seq experiment. Azimuth leverages reference based mapping, pipeline that inputs counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression. All results can be explored within the app, and easily downloaded for additional downstream analysis.

Proper citation: Azimuth (RRID:SCR_021084) Copy   

•   Source: SciCrunch Registry