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3DBar (RRID:SCR_008896)


http://www.3dbar.org

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML


Keywords

3d, reconstruction, brain structure, brain, algorithm or reusable library, web service, atlas application, three dimensional display, spinal cord, sensory system, waxholm space

Resource ID

SCR_008896

Alternate IDs

nlx_151380

Website Status

Last checked up

Abbreviation(s)

3dBAR

Species

mouse, macaque, human, rhesus monkey

Resource Type

Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Availability

GNU General Public License

Synonym(s)

3d Brain Atlas Reconstructor, 3D BAR

Proper citation

3DBar, RRID:SCR_008896

Alternate URLs

http://www.nitrc.org/projects/bar3d, http://service.3dbar.org, http://www.3dbar.org:8080/, http://3dbar.org

Reference

PMID:22227717

Other resources frequently mentioned in the literature with this resource

SciCrunch Registry

Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch are assigned RRIDs which are used to cite resources in scientific manuscripts.

Common atlas format and 3D brain atlas reconstructor: infrastructure for constructing 3D brain atlases.

  • Majka P
  • Neuroinformatics
  • 2012 Apr 22

One of the challenges of modern neuroscience is integrating voluminous data of diferent modalities derived from a variety of specimens. This task requires a common spatial framework that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume. The 3D atlases available so far have been created using frameworks which make it difficult for other researchers to replicate the results. To facilitate reproducible research and data sharing in the field we propose an SVG-based Common Atlas Format (CAF) to store 2D atlas delineations or other compatible data and 3D Brain Atlas Reconstructor (3dBAR), software dedicated to automated reconstruction of three-dimensional brain structures from 2D atlas data. The basic functionality is provided by (1) a set of parsers which translate various atlases from a number of formats into the CAF, and (2) a module generating 3D models from CAF datasets. The whole reconstruction process is reproducible and can easily be configured, tracked and reviewed, which facilitates fixing errors. Manual corrections can be made when automatic reconstruction is not sufficient. The software was designed to simplify interoperability with other neuroinformatics tools by using open file formats. The content can easily be exchanged at any stage of data processing. The framework allows for the addition of new public or proprietary content.

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