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https://biccn.org

Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.

Proper citation: BICCN (RRID:SCR_015820) Copy   

•   Source: SciCrunch Registry
  

https://biccn.org/teams/u01-fischl

Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.

Proper citation: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) Copy   

•   Source: SciCrunch Registry
  

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells

MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.

Proper citation: MapMyCells (RRID:SCR_024672) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README

Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays. Developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.

Proper citation: Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) Copy   

•   Source: SciCrunch Registry
  

https://knowledge.brain-map.org/celltypes

Software application to examine multimodal data from thousands of cells across 3 mammalian species.

Proper citation: Cell Type Knowledge Explorer (RRID:SCR_022793) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner

Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement.

Proper citation: mBrainAligner (RRID:SCR_022791) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/snm3C/README

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.

Proper citation: snm3C Pipeline (RRID:SCR_025041) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/ATAC/README

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.

Proper citation: ATAC Pipeline (RRID:SCR_024656) Copy   

•   Source: SciCrunch Registry
  

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

Software package for massive single cell data processing. Enables analysis of million scale single cell RNA-seq data and is functionally comparable to Seurat and SCANPY. Command line tool, Python package and base for Cloud based analysis workflows. Supports variety of analysis tasks, such as cell and gene level quality control, highly variable gene selection, dimension reduction, kNN graph building, data integration, clustering, differential expression analysis and putative cell type annotation.

Proper citation: Pegasus (RRID:SCR_021645) Copy   

•   Source: SciCrunch Registry
  

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

Web interactive visualization tool for large scale single cell genomics data.Interactive web application for exploring million scale single cell datasets. Can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on personal computer. Consists of client side component implemented in JavaScript and server component implemented in Python. Client uses React to manage state and WebGL to visualize variables on 2D/3D embeddings in performant manner. Server component consists of functions to manage datasets, slice variables from dataset stored in PARQUET, Zarr or H5AD formats.

Proper citation: Cirrocumulus (RRID:SCR_021646) Copy   

•   Source: SciCrunch Registry
  

http://www.brain-map.org

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.

Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy   

•   Source: SciCrunch Registry
  

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry
  

https://github.com/AllenInstitute/AllenSDK

Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.

Proper citation: Allen Software Development Kit (RRID:SCR_018183) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/Multiome_Pipeline/README

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.

Proper citation: Multiome Pipeline (RRID:SCR_024217) Copy   

•   Source: SciCrunch Registry
  

https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas

Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression.

Proper citation: Allen Brain Cell Atlas (RRID:SCR_024440) Copy   

•   Source: SciCrunch Registry
  

https://terra.bio

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.

Proper citation: Terra (RRID:SCR_021648) Copy   

•   Source: SciCrunch Registry
  

https://knowledge.brain-map.org/data?fprogram.title=BRAIN%20Initiative%20Cell%20Census%20Network&limit=25&offset=0&sortDirection=ASC&sortProperty=species.name

BRAIN Initiative Cell Census Network data catalog. Provides access to all major data sets of the BICCN with descriptions.

Proper citation: Allen Brain Map BICCN Data Catalog (RRID:SCR_022815) Copy   

•   Source: SciCrunch Registry
  

https://singlecell.broadinstitute.org/single_cell?scpbr=biccn-anatomy-and-morphology-project

Joint effort with Brain Architecture Portal and Single Cell Portal to visually combine anatomic and molecular brain data in. Users can search for neuroscience data using natural language and faceted search, and then this portal retrieves molecular data housed in the Single Cell Portal and anatomical data in the Brain Architecture Portal. Each study includes information on cell types, gene expression, related genes, and spatial transcriptomics. You can also download a study’s data to explore further and build on your science.

Proper citation: BICCN Anatomy and Morphology Project (RRID:SCR_021647) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/PairedTag_Pipeline/README

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.

Proper citation: Paired-Tag Pipeline (RRID:SCR_025042) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/BuildIndices_Pipeline/README

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).

Proper citation: BuildIndices (RRID:SCR_027630) Copy   

•   Source: SciCrunch Registry