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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://github.com/zhenzonglei/abat

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

Proper citation: Allen Brain Atlas Tools (RRID:SCR_023855) 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
  

https://web.ece.ucsb.edu/~riichirohira/TopBM-2.06/index.html

Web interactive visualization tool of brain architecture based on tracer database.There are four modes of visualization: surfarce, flat, coronal, and saggital.

Proper citation: BrainModules (RRID:SCR_023850) Copy   

•   Source: SciCrunch Registry
  

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
  

http://mouse.brain-map.org/static/atlas

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy   

•   Source: SciCrunch Registry
  

http://transgenicmouse.alleninstitute.org/

A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridization (DFISH), native fluorescence of XFP (generic term for fluorescent proteins of different colors), and immunohistochemical (IHC) labeling of marker genes.

Proper citation: Allen Institute for Brain Science Transgenic Mouse Study (RRID:SCR_002999) 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://atlas.brain-map.org/

3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

Proper citation: Allen Mouse Brain Common Coordinate Framework (RRID:SCR_020999) 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
  

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
  

http://mouse.brain-map.org/

Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.

Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy   

•   Source: SciCrunch Registry
  

https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq

Collection of data set including single cell transcriptomes from multiple cortical areas and hippocampal formation. Samples were collected from dissections of brain regions from  8 week old male and female mice, primarily from pan GABAergic, pan glutamatergic, and pan neuronal transgenic lines, with addition of more specific transgenic lines and some retrogradely labeled cells in VISp and ALM.

Proper citation: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq (RRID:SCR_019013) Copy   

•   Source: SciCrunch Registry
  

https://github.com/chrisgorgo/alleninf

Software package to test hypotheses about relation of patterns found in statistical maps with gene expression measured in postmortem brains. Refines corregistration coordinates provided by the Allen Institute.Used to compare statistical map of brain with gene expression patterns from Allen Human Brain Atlas.

Proper citation: Alleninf (RRID:SCR_023837) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cortex-lab/allenCCF

Software tools to work with Allen Inst CCF data in Matlab. MATLAB code to work with the Allen Mouse Brain CCF data.

Proper citation: allenCCF (RRID:SCR_023830) Copy   

•   Source: SciCrunch Registry
  

https://github.com/brainglobe/morphapi

Software Python package for downloading neurons 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.

Proper citation: MorphAPI (RRID:SCR_023851) 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