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BICCN Working Groups

Working groups comprise members of the BICCN consortium working on advanced protocols and standards for uncovering the cellular make-up of the brain. BICCN Working Groups span the core set of activities that require accurate documentation in protocol, metadata, and feature description. Activities include write up of all protocols across laboratories for comparison and future reference for analysis discrepancies. Another key charge is in the determination of appropriate features and data resolution relevant to cell type and to be reported to BCDC.

 

 

 

BICCN 2.0 Whole Mouse Brain WG.   Chairs: Eran Mukamel, UCSD, Hongkui Zeng, Allen Institute

Charter

Deliverables
  • Data integration for transcriptomic & epigenomic data across entire mouse brain and spinal cord
  • Pipeline processing
  • Collaborative analysis to support the creation of a cell census and consortium publication(s)
  • Support FAIR data standards
  • Create high impact outputs of the scientific work
  • Omics standards
  • Sample level QC
  • Sequence data mapping
  • Cell level standards 
  • Cluster level standards
  • Uniform pipelines and BICCN Whole Mouse Brain Workspace
  • Terra workspace

 

 

 

BICCN 2.0 Cell-Type Specific Enhancers.  Chairs: Bosiljka Tasic, Allen Institute, Bing Ren, UCSD

Charter

Deliverables
  • Develop methods to identify cell-type specific enhancers that can drive systemic delivery of reporter genes to select subclasses or types of brain cells in mice and primates.
  • Obtain experimental data to support the validity of these methods.
  • Single-cell multiomic atlases of the primary motor cortex in mice and primates
  • Computational tools for predicting brain cell-type specific enhancers
  • Experimentally validated enhancers active in select cortical neuronal sub-types

 

 

 

BICCN Infrastructure & Metadata WG.  Chairs: Carol Thompson, Allen Institute, Mike Hawrylycz, Allen Institute

Charter

Deliverables
  • Data standards
  • Data collection processes and reporting
  • BICCN infrastructure ecosystem improvements
  • Support FAIR data standards

 

 

 

BICCN Morphology WG. Chairs: Giorgio Ascoli, GMU, Hanchuan Peng, SEU-Allen Joint Center

Charter

Deliverables
  • Morphology metadata
  • Data formats
  • Standards
  • CCF mapping
  • Reconstructions
  • Community usage
  • Standardized on NIFTI and SWC data formats
  • Standard metadata file (metainfo.txt)
  • fMOST QC checks via Data Core.
    • Data quality
    • Reconstruction difficulty assessment
  • Reference annotation and reference terminologies
    • CCF 3.0 visualization
    • JSON format for soma locations and projection targets
  • Standardized inventory of BICCN cell morphologies

 

 

 

BICCN 2.0 Molecular Wiring Diagrams Working Group WG. Chair: Hongwei Dong

Charter

Deliverables
  • Begin planning on BICCN 2.0 project on Molecularly Annotated Wiring Diagrams of the Mammalian Brain
  • Finalize the mini-atlas joint anatomy paper
  • Mapping of internal metadata to BIL standard metadata
  • QC checks via Data Core.
    • Completeness of files and datasets
  • Registration software input/output metadata standards
    • NRRD
    • Sidecar JSON file
    • VTK for low res, JP2000, TIFF for high res compressed/uncompressed images

 

 

 

BICCN Mini-Atlas Flagship Publication WG. Chairs: Joe Ecker, Salk Institute, Hongkui Zeng, Allen Institute, John Ngai, NIH

Charter

Deliverables
  • Planning, coordinating and writing the mini-atlas flagship paper.
  • Supporting FAIR data standards in the mini-atlas paper and across companion papers.

Complete

 

 

 

BICCN Human & NHP WG. Chairs: Ed Lein, Allen Institute, Arnold Kriegstein, UCSF

Charter

Deliverables
  • Coordination on regional sampling plans
  • Methods comparisons
  • Scope out future big human and NHP atlasing
  • Joint comparative analysis

Active

 

 

 

BICCN 2.0 Developing Brain Atlas WG. Chairs: Paola Arlotta, Harvard University, Tomasz Nowakowski, UCSF

Charter

Deliverables
  • Mouse, human, and NHP development

Active

 

 

 

BICCN 2.0 Proteomic Brain Atlas WG. Chairs: Kwanghun Chung, MIT and Elizabeth Hillman, Columbia University

Charter

Deliverables
  • Technology platform development
  • Proteomic data acquisition and integration
  • Collaborative analysis
  • Technology, reagents, protocols, and data dissemination