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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 scene from the live preview interface with selected models of structures from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/): brain stem (brown), cerebellum (yellow), cerebral nuclei (blue) and cerebral cortex (green, transparent). See text for description of highlighted regions (a–f)
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Fig4: Example scene from the live preview interface with selected models of structures from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/): brain stem (brown), cerebellum (yellow), cerebral nuclei (blue) and cerebral cortex (green, transparent). See text for description of highlighted regions (a–f)

Mentions: Figure 4 shows an example live preview window with a set of reconstructions from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/). The user has a wide range of interaction options available. He or she can look for and display structures from the hierarchy tree (Fig. 4a), search for a particular structure from the list of structures using auto complete function (Fig. 4b), zoom the scene in and out, rotate the models, apply transparency, load multiple structures based on the hierarchy (Fig. 4c), see the structures from different angles, apply predefined viewpoints (right, left, anterior, posterior, superior, inferior, perspective, etc.; Fig. 4d), read out the coordinates of the location pointed by the mouse cursor (Fig. 4e). All models currently loaded are listed below the preview window as tiles summarizing precalculated reconstructions which are ready for immediate download (Fig. 4f). The tiles include the visualization (thumbnail) and download links for polygonal mesh and volumetric mask in both high and low reconstruction preset.Fig. 4


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 scene from the live preview interface with selected models of structures from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/): brain stem (brown), cerebellum (yellow), cerebral nuclei (blue) and cerebral cortex (green, transparent). See text for description of highlighted regions (a–f)
© Copyright Policy
Related In: Results  -  Collection

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

Fig4: Example scene from the live preview interface with selected models of structures from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/): brain stem (brown), cerebellum (yellow), cerebral nuclei (blue) and cerebral cortex (green, transparent). See text for description of highlighted regions (a–f)
Mentions: Figure 4 shows an example live preview window with a set of reconstructions from the Allen Mouse Brain Reference Atlas (http://mouse.brain-map.org/). The user has a wide range of interaction options available. He or she can look for and display structures from the hierarchy tree (Fig. 4a), search for a particular structure from the list of structures using auto complete function (Fig. 4b), zoom the scene in and out, rotate the models, apply transparency, load multiple structures based on the hierarchy (Fig. 4c), see the structures from different angles, apply predefined viewpoints (right, left, anterior, posterior, superior, inferior, perspective, etc.; Fig. 4d), read out the coordinates of the location pointed by the mouse cursor (Fig. 4e). All models currently loaded are listed below the preview window as tiles summarizing precalculated reconstructions which are ready for immediate download (Fig. 4f). The tiles include the visualization (thumbnail) and download links for polygonal mesh and volumetric mask in both high and low reconstruction preset.Fig. 4

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