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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://github.com/RobertoDF/BRIO
Software visualization and analysis tool based on the Allen Brain Atlas connectivity database. Produces custom visualizations and figures for input output strength of specific brain area.
Proper citation: BRain area Input Output (RRID:SCR_023846) Copy
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
https://github.com/Nexusger/AllenMouseBrainImageLoader
Respository contains two small software tools which render annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial).
Proper citation: Allen Mouse Brain ImageLoader (RRID:SCR_023827) Copy
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
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
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
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
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
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
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
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
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
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
https://github.com/ejcorn/mouse_abi_tool
Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.
Proper citation: Mouse_abi_tool (RRID:SCR_023831) Copy
https://github.com/liqihang007/VIS_STEB
Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data.
Proper citation: Spatiotemporal pattern Exploration of Brain (RRID:SCR_023825) Copy
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