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3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

Majka P, Kowalski JM, Chlodzinska N, Wójcik DK - Neuroinformatics (2013)

Bottom Line: An application programming interface (API) facilitates programmatic access to the service contents from other websites.The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large.The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

View Article: PubMed Central - PubMed

Affiliation: Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093, Warsaw, Poland, p.majka@nencki.gov.pl.

ABSTRACT
Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

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Example of 3dBAR’s data interoperability. Labeled volume of macaque’s brain (Bowden and Dubach 2003) loaded into ITK-SNAP (Yushkevich et al. 2006). Note that the structures’ names, abbreviations and colors are consistent among different forms of the reconstructions throughout the service
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Fig3: Example of 3dBAR’s data interoperability. Labeled volume of macaque’s brain (Bowden and Dubach 2003) loaded into ITK-SNAP (Yushkevich et al. 2006). Note that the structures’ names, abbreviations and colors are consistent among different forms of the reconstructions throughout the service

Mentions: Apart from reconstructions representing individual structures or subsets of all structures, two kinds of datasets carry all delineations available within a given atlas. The first one is a NIfTI file with labeled volume based on the atlas. In addition to the volume, a look-up table is provided which contains a mapping from the label index to the corresponding structure’s name, color etc. This allows the labeled volume to be used with a wide range of neuroimaging software like 3d Slicer (http://www.slicer.org/; Pieper et al. 2004), ITK-SNAP (Yushkevich et al. 2006) or similar (Fig. 3). Another type of dataset containing all the data constituting the atlas is the Common Atlas Format (CAF) dataset from which all the reconstructions originate (see the “Implementation” section). Because of that, names, abbreviations, colors, etc. are consistent among the different formats. All the types of reconstructions and datasets including those containing the whole atlas are available for every atlas regardless of its source form (either 2D or 3D).Fig. 3


3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

Majka P, Kowalski JM, Chlodzinska N, Wójcik DK - Neuroinformatics (2013)

Example of 3dBAR’s data interoperability. Labeled volume of macaque’s brain (Bowden and Dubach 2003) loaded into ITK-SNAP (Yushkevich et al. 2006). Note that the structures’ names, abbreviations and colors are consistent among different forms of the reconstructions throughout the service
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3824210&req=5

Fig3: Example of 3dBAR’s data interoperability. Labeled volume of macaque’s brain (Bowden and Dubach 2003) loaded into ITK-SNAP (Yushkevich et al. 2006). Note that the structures’ names, abbreviations and colors are consistent among different forms of the reconstructions throughout the service
Mentions: Apart from reconstructions representing individual structures or subsets of all structures, two kinds of datasets carry all delineations available within a given atlas. The first one is a NIfTI file with labeled volume based on the atlas. In addition to the volume, a look-up table is provided which contains a mapping from the label index to the corresponding structure’s name, color etc. This allows the labeled volume to be used with a wide range of neuroimaging software like 3d Slicer (http://www.slicer.org/; Pieper et al. 2004), ITK-SNAP (Yushkevich et al. 2006) or similar (Fig. 3). Another type of dataset containing all the data constituting the atlas is the Common Atlas Format (CAF) dataset from which all the reconstructions originate (see the “Implementation” section). Because of that, names, abbreviations, colors, etc. are consistent among the different formats. All the types of reconstructions and datasets including those containing the whole atlas are available for every atlas regardless of its source form (either 2D or 3D).Fig. 3

Bottom Line: An application programming interface (API) facilitates programmatic access to the service contents from other websites.The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large.The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

View Article: PubMed Central - PubMed

Affiliation: Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093, Warsaw, Poland, p.majka@nencki.gov.pl.

ABSTRACT
Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

Show MeSH
Related in: MedlinePlus