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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) | atlas, data or information resource | 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. | Anatomical labels, Allen Common Coordinate Framework, Franklin and Paxinos labels, MRI atlas, segment labels, transgenic mice, dorsal striatum, cortico-striatal connectivity data, mouse brain anatomical structure |
is used by: BICCN is related to: Allen Institute for Brain Science |
NIH Office of the Director R24 OD018559; NIMH R01 MH116176; NINDS R01 NS10 8407; Pennsylvania Department of Health |
PMID:31699990 | Free, Freely available | SCR_019267 | SciCrunch Registry | 2026-10-24 12:51:15 | 2 | ||||||||
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Allen Institute for Brain Science Resource Report Resource Website 500+ mentions |
Allen Institute for Brain Science (RRID:SCR_006491) | atlas, data or information resource, portal, topical portal | Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain. | Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomy |
is listed by: Brain Architecture Project is related to: VisiGene Image Browser is related to: Recombinase (cre) Activity is related to: Cytosplore Viewer is related to: Mozak is related to: Microns Explorer is related to: CellLocator is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: Atlasplot is related to: Atlas Ontology Model is related to: Allen Brain Atlas-Driven Visualizations is related to: Brain heatmap is related to: Brainmapr is related to: ABAEnrichment is related to: Hippo-ATESC is related to: AllenDigger is related to: Cocoframer is related to: Process Genes List is related to: AIDAhisto is related to: MeshGen is related to: PET-CT mouse brain toolbox is related to: Multimodal Environment for Neuroimaging and Genomic Analysis is related to: goi2roimapping is related to: Spatiotemporal pattern Exploration of Brain is related to: Allen Mouse Brain ImageLoader is related to: ARA Tools is related to: allenCCF is related to: CutNII is related to: Genomic-and-High-Dimensional-Data is related to: Mouse_abi_tool is related to: Abagen is related to: VoxHunt is related to: ABI-expression-data-generator is related to: GCEA_FalsePositives is related to: Atlas Splitter is related to: ABAnnotate is related to: JuGEx is related to: Alleninf is related to: Atlas Alignment Meter is related to: Pinpoint is related to: Atlas Densities is related to: Atlas Direction Vectors is related to: SageBionetworks Portals is related to: brain-mapping is related to: BrainModules is related to: BrainRegionMarkers is related to: AP-histology is related to: Brainreg-segment is related to: Segmenting Brain Regions is related to: DeepSlice is related to: Cell Type Analysis Toolbox is related to: BrainGlobe Atlas API is related to: QUINT is related to: BRain area Input Output is related to: Brainreg is related to: MorphAPI is related to: Aligning Big Brains and Atlases is related to: Allen Brain Atlas Tools is related to: Brain Gene Expression Analysis toolbox is related to: Blue Brain Cell Atlas is related to: 3DBar is related to: Brainrender is related to: QuickNII is related to: Brain Architecture Project is related to: NeuroInfo is related to: Azimuth is related to: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas is related to: Integrated Brain Gene Expression is related to: MIRACL is related to: Linked Neuron Data is related to: BrainStars is related to: MouseLight Project is related to: Distributed Archives for Neurophysiology Data Integration is related to: Open Source Brain is related to: VisuAlign is related to: NS-Forest is related to: SHARCQ is related to: ModelDB is related to: Gene Expression Omnibus (GEO) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: CellFinder is related to: Nutil - Neuroimaging utilities is related to: NeuroMorpho.Org is related to: Semi-Manual Alignment to Reference Templates is related to: MeshView is related to: Single Cell Portal is related to: Brain Image Library is related to: UCSC Cell Browser is related to: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is related to: cellxgene is related to: Atlas Ontology Model has parent organization: Allen Institute is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Institute for Brain Science Sleep Study is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Institute for Brain Science Transgenic Mouse Study is parent organization of: Allen Institute Neurowiki is parent organization of: Ivy Glioblastoma Atlas Project is parent organization of: Allen Brain Atlas API is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: Allen Institute Mouse Diversity Study is parent organization of: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: ABA Adult Mouse Brain Ontology is parent organization of: NIH Blueprint NHP Atlas is parent organization of: Aging Dementia and Traumatic Brain Injury Study is parent organization of: ACQ4 is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas is parent organization of: BRAIN Cell Data Center is parent organization of: BICCN Cell Registry is parent organization of: ABA Mouse Brain: Atlas is parent organization of: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Allen Mouse Reference Atlas Ontology is parent organization of: BICCN is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: Brain Knowledge Platform |
nif-0000-00146 | SCR_006491 | SciCrunch Registry | The Allen Institute for Brain Science, Allen Mouse Brain | 2026-10-24 12:49:07 | 803 | |||||||||
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BuildIndices Resource Report Resource Website 1+ mentions |
BuildIndices (RRID:SCR_027630) | software resource, software toolkit | Software workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). | check inputs, modify reference files, create STAR index, calculate chromosome sizes, |
has parent organization: Broad Institute is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | SCR_027630 | SciCrunch Registry | 2026-10-24 12:54:26 | 1 | ||||||||||
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CellLocator Resource Report Resource Website 1+ mentions |
CellLocator (RRID:SCR_019264) | software application, software resource | Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas. | Desktop application based on 3D Slicer, mapping samples into common 3D spaces, Allen Institute for Brain Science CCF, MNI atlas, color segmented by structure of brain, create planar polyline annotation |
is used by: BICCN has parent organization: Allen Institute |
Free, Available for download, Freely available | SCR_022792 | https://cell-locator.readthedocs.io/en/latest/ | SCR_019264 | SciCrunch Registry | cell-locator, BICCN Cell Locator, CellLocator by Allen Institute | 2026-10-24 12:51:50 | 3 | |||||||
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Paired-Tag Pipeline Resource Report Resource Website 1+ mentions |
Paired-Tag Pipeline (RRID:SCR_025042) | data processing software, software application, software resource | Software open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of 3' single-nucleus histone modification data (generated with the paired-tag protocol]) and 10x gene expression (GEX) data generated with the 10x Chromium Multiome assay. | data processing, 10x Genomics Multiome assay data, single-cell data, single nucleus gene expression data, single-nucleus histone modification data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/paired_tag | SCR_025042 | SciCrunch Registry | Paired-Tag Pipeline, paired_tag, Paired-Tag | 2026-10-24 12:53:29 | 1 | ||||||||
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Multiome Pipeline Resource Report Resource Website 1+ mentions |
Multiome Pipeline (RRID:SCR_024217) | data processing software, software application, software resource | Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay. | data processing, 10x Genomics Multiome assay data, single cell data, single nucleus gene expression data, single cell chromatin accessibility data, |
is organization facet of: BRAIN Initiative Cell Atlas Network is organization facet of: BICCN is organization facet of: SCORCH |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/multiome | SCR_024217 | SciCrunch Registry | , Multiome GEX and scATAC Pipeline, Multiome Pipeline | 2026-10-24 12:49:39 | 1 | ||||||||
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ATAC Pipeline Resource Report Resource Website |
ATAC Pipeline (RRID:SCR_024656) | data analysis software, data processing software, software application, software resource | Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin), a technique used in molecular biology to assess genome-wide chromatin accessibility. | data processing, 10x Genomics Multiome ATAC-seq assay data, single-cell data, single-cell chromatin accessibility assay data |
is related to: BICCN is related to: SCORCH has parent organization: Broad Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/multiome/atac.wdl | SCR_024656 | SciCrunch Registry | ATAC, atac, atac pipeline | 2026-10-24 12:49:43 | 0 | ||||||||
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snm3C Pipeline Resource Report Resource Website 1+ mentions |
snm3C Pipeline (RRID:SCR_025041) | snM3C | data processing software, software application, software resource | Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics. | data processing, single-nucleus methylome data, single-cell data, chromatin contact data, single-cell methylome and chromatin contact sequencing data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/snM3C | SCR_025041 | SciCrunch Registry | , Single Nucleus Methly-Seq and Chromatin Capture, single-nucleus Methylome and Chromatin Contact, Single Nucleus Methly-Seq and Chromatin Capture (snM3C) | 2026-10-24 12:53:29 | 2 | |||||||
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Terra Resource Report Resource Website 50+ mentions |
Terra (RRID:SCR_021648) | data or information resource, portal | Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy. | Biomedical researcher platform, access data, run analysis tools, collaborate, access controlled datasets, cloud repositories |
is used by: BRAIN Initiative Cell Atlas Network lists: Cumulus lists: Pegasus lists: Broad Terra cloud commons for pathogen surveillance has parent organization: Broad Institute has organization facet: scATAC Pipeline has organization facet: Smart-seq2 Single Nucleus Multi Sample Pipeline has organization facet: CEMBA MethylC Seq Pipeline has organization facet: Smart-seq2 Multi-Sample Pipeline is organization facet of: BICCN is organization facet of: Single Cell Portal |
NIMH U24 MH130968 | Free, Freely available | SCR_021648 | SciCrunch Registry | Terra Cloud Native Platform, BCDC cloud computing environment | 2026-10-24 12:48:57 | 90 | ||||||||
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cellxgene Resource Report Resource Website 50+ mentions |
cellxgene (RRID:SCR_021059) | data processing software, data visualization software, software application, software resource | 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. | Single cell transcriptomics datasets explorer, gene expression visualization, identify cell types, identify diseases, plotting gene expression level |
is used by: BICCN is related to: Allen Institute for Brain Science |
Free, Available for download, Freely available | https://github.com/chanzuckerberg/cellxgene | SCR_021059 | SciCrunch Registry | 2026-10-24 12:48:49 | 82 |
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