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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://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

http://www.informatics.jax.org/home/recombinase

Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.

Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) 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://dandiarchive.org

Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles.

Proper citation: Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) 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

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/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://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://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

http://neuromorpho.org/index.jsp

Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

Proper citation: NeuroMorpho.Org (RRID:SCR_002145) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/ATOM?p=classes&conceptid=root

Ontology for describing key metadata elements of spatial reference atlases. Ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures. Identifies and defines relationships between four common atlases and characterizes their properties and organization. This model can serve as suggestion for minimum requiremens for atlases and will accelerate neuroscience data integration.

Proper citation: Atlas Ontology Model (RRID:SCR_023499) Copy   

•   Source: SciCrunch Registry

https://abagen.readthedocs.io/en/stable/

Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data.

Proper citation: Abagen (RRID:SCR_023832) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/allen-atlas-brain-toolbox

Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.

Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy   

•   Source: SciCrunch Registry