COBMAN: Comprehensive Open Brain Map Archive Network

COBMAN  is a network of FTP and web servers around the world that store identical, up-to-date, versions of anatomical experiments and data submitted to be displayed on openbrainmap.org.

COBMAN preferentially accepts experiments that have already been subjected to peer-review and only in rare occasions data will be considered before peer-review. In cases a user needs to share ongoing projects and data with reviewers or collaborators we refer to our pre-publication FTP.

When submitting anatomical data to COBMAN several standards need to be followed. The user needs to generate the following 3 content types for each individual brain:

  1. Specification of meta data:
    • First authors and Principal Investigator contact details
    • Short description or abstract of the data
    • DOI or link to published article
    • Mouse ID
    • Age of mouse at experiment termination
    • Sex
    • Line (if transgenic include link to source Jax/Gensat etc.)
    • Expression system (fluorescent proteins, IHC, ISH).
    • Vector or probe (if any).
    • Target coordinates (if any)
    • Microscope used (system and imaging sensor)
    • Optics (magnification factor and numerical aperature).
    • Theoretical pixel resolution.
  2. Data:
    • A scroll reel rendered in the coronal plane with all included sections.
    • Raw 16 bit TIFF data (stitched).
    • RosettaJSON files for each section.
    • R list objects from segment(), registration(), and get.cell.ids() output saved as one .Rdata file per section.
  3. Legal:
    • Statement of approval from ethical committee.

To submit a project start by filling out this form (link to be posted) and you'll get FTP login details in the email for uploading your data using WholeBrain R package.

WholeBrain R package include a set of commands that will greatly facilitate generation of data for submission.

More instructions to follow.