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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.opensourcebrain.org

A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.

Proper citation: Open Source Brain (RRID:SCR_001393) Copy   

•   Source: SciCrunch Registry

https://chanzuckerberg.com/science/programs-resources/single-cell-biology/cellxgene/

Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter.

Proper citation: cellxgene (RRID:SCR_021059) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nutil/

Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow.

Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) 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://www.ncbi.nlm.nih.gov/geo/

Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) 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://www.linked-neuron-data.org/

Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.

Proper citation: Linked Neuron Data (RRID:SCR_003658) 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://bbp.epfl.ch/nexus/cell-atlas/

Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access.

Proper citation: Blue Brain Cell Atlas (RRID:SCR_019266) Copy   

•   Source: SciCrunch Registry

http://kimlab.io/brain-map/atlas/

Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.

Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/explore/seattle-alzheimers-disease

Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute.

Proper citation: Seattle Alzheimer Disease Brain Cell Atlas (RRID:SCR_023110) 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://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