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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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Related in: MedlinePlus

Benchmarking and quality assessment of the service. Box and whisker plots showing order statistics (5 % percentile, lower quartile, median, upper quartile and 95 % percentile) for 197 structures from datasets based on the Waxholm Space mouse brain template. a Time elapsed of an initial reconstruction (No cache) in comparison with consecutive reconstructions (With cache) performed using high quality pipeline. b Mesh discrepancy in comparison with unprocessed mesh for high quality pipeline (HQ) and low quality pipeline (LQ). c Comparison of the ratio of vertices from meshes generated with low- and high quality pipeline with respect to the number of vertices in the unprocessed mesh
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Fig2: Benchmarking and quality assessment of the service. Box and whisker plots showing order statistics (5 % percentile, lower quartile, median, upper quartile and 95 % percentile) for 197 structures from datasets based on the Waxholm Space mouse brain template. a Time elapsed of an initial reconstruction (No cache) in comparison with consecutive reconstructions (With cache) performed using high quality pipeline. b Mesh discrepancy in comparison with unprocessed mesh for high quality pipeline (HQ) and low quality pipeline (LQ). c Comparison of the ratio of vertices from meshes generated with low- and high quality pipeline with respect to the number of vertices in the unprocessed mesh

Mentions: The reconstruction process is a crucial element of the service’s functionality. The process is triggered by the web server and executed on the computational cluster. As a result, we obtain models, which may consist of one or many structures, and which may be delivered in one or many output formats. The reconstruction request initiated by the server carries (1) a list of structures to be reconstructed, (2) a pipeline that will be used to perform the reconstruction, and (3) the output formats in which the results are to be available. The request is then dispatched by the computational cluster manager to computation nodes so that many reconstructions can be performed simultaneously. On each node a 3dBAR reconstruction module is executed. It checks if a structure to be reconstructed already exists. If that is the case, no actual reconstruction is performed, only a database entry is made that references the existing model with the currently processed request. That allows to avoid model duplications and significantly reduces reconstruction time and resources consumption (Fig. 2a).Fig. 2


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

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

Benchmarking and quality assessment of the service. Box and whisker plots showing order statistics (5 % percentile, lower quartile, median, upper quartile and 95 % percentile) for 197 structures from datasets based on the Waxholm Space mouse brain template. a Time elapsed of an initial reconstruction (No cache) in comparison with consecutive reconstructions (With cache) performed using high quality pipeline. b Mesh discrepancy in comparison with unprocessed mesh for high quality pipeline (HQ) and low quality pipeline (LQ). c Comparison of the ratio of vertices from meshes generated with low- and high quality pipeline with respect to the number of vertices in the unprocessed mesh
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: Benchmarking and quality assessment of the service. Box and whisker plots showing order statistics (5 % percentile, lower quartile, median, upper quartile and 95 % percentile) for 197 structures from datasets based on the Waxholm Space mouse brain template. a Time elapsed of an initial reconstruction (No cache) in comparison with consecutive reconstructions (With cache) performed using high quality pipeline. b Mesh discrepancy in comparison with unprocessed mesh for high quality pipeline (HQ) and low quality pipeline (LQ). c Comparison of the ratio of vertices from meshes generated with low- and high quality pipeline with respect to the number of vertices in the unprocessed mesh
Mentions: The reconstruction process is a crucial element of the service’s functionality. The process is triggered by the web server and executed on the computational cluster. As a result, we obtain models, which may consist of one or many structures, and which may be delivered in one or many output formats. The reconstruction request initiated by the server carries (1) a list of structures to be reconstructed, (2) a pipeline that will be used to perform the reconstruction, and (3) the output formats in which the results are to be available. The request is then dispatched by the computational cluster manager to computation nodes so that many reconstructions can be performed simultaneously. On each node a 3dBAR reconstruction module is executed. It checks if a structure to be reconstructed already exists. If that is the case, no actual reconstruction is performed, only a database entry is made that references the existing model with the currently processed request. That allows to avoid model duplications and significantly reduces reconstruction time and resources consumption (Fig. 2a).Fig. 2

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