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Virtual Fly Brain icon

Virtual Fly Brain, or VFB, is an interactive, web-based tool that allows neurobiologists to explore the detailed neuroanatomy, transgene expression and associated phenotypes of the Drosophila melanogaster brain.^[1] Users can browse painted 3D image stacks of the Drosophila brain, choosing any plane of section they want and clicking on painted regions to find names' definitions, references and synonyms for the chosen region. For each region, they can run queries to find neurons, transgene expression and phenotypes. For each neuron found, users can browse definitions, references and synonyms.

Technical details

Virtual Fly Brain uses an ontological model of Drosophila anatomy written in OWL2 and based on the Drosophila literature. This contains detailed information about both gross neuroanatomy, neuron classes and the relationships between them. Underlying each neuroanatomy query is a query of this ontology in OWL-DL.

Queries of phenotype and expression utilise the large volume of expression and phenotype data in FlyBase^[2] annotated using the Drosophila anatomy ontology. Each expression or phenotype query starts with a query of the anatomy ontology for terms appropriate to the chosen region. The output of this query is then used as input for a query of the FlyBase chado^[3] database for expression or phenotype annotated using these terms.

Images in the viewer are delivered as a series of tiles covering only the visible area in the browser window. The tiles are produced from a compound 3D Woolz^[4]^[5] object representing the overall structure and individual painted domains.

References

^ http://www.virtualflybrain.org/
^ R, Drysdale; FlyBase Consortium (2008). "FlyBase : a database for the Drosophila research community". Methods Mol. Biol. 420: 45–59. doi:10.1007/978-1-59745-583-1_3. PMID 18641940. {{cite journal}}: |access-date= requires |url= (help); Invalid |ref=harv (help)
^ "Chado - Getting Started". GMOD. 13 February 2014. Retrieved 2017-06-09.
^ "Woolz Image Processing: Woolz Core Software". EMAP Home. Retrieved 2017-06-09.
^ https://github.com/ma-tech/Woolz

External links

[1] ttp://www.virtualflybrain.org/

[2] R, Drysdale; FlyBase Consortium (2008). "FlyBase : a database for the Drosophila research community". Methods Mol. Biol. 420: 45–59. doi:10.1007/978-1-59745-583-1_3. PMID 18641940. {{cite journal}}: |access-date= requires |url= (help); Invalid |ref=harv (help)

[3] "Chado - Getting Started". GMOD. 13 February 2014. Retrieved 2017-06-09.

[4] "Woolz Image Processing: Woolz Core Software". EMAP Home. Retrieved 2017-06-09.

[5] ttps://github.com/ma-tech/Woolz

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 [[Image:flyBrain.gif|frame|alt=VFB logo|Virtual Fly Brain icon]]
-'''Virtual Fly Brain''', or '''VFB''', is an interactive, web-based tool that allows neurobiologists to explore the detailed neuroanatomy, transgene expression and associated phenotypes of the ''[[Drosophila melanogaster]]'' brain.<ref>http://www.virtualflybrain.org/</ref> Users can browse painted 3D image stacks of the ''Drosophila'' brain, choosing any plane of section they want and clicking on painted regions to find names' definitions, references and synonyms for the chosen region.  For each region, they can run queries to find neurons, transgene expression and phenotypes.  For each neuron found, users can browse definitions, references and synonyms.
+'''Virtual Fly Brain''', or '''VFB''', is an interactive, web-based tool that allows neurobiologists to explore the detailed neuroanatomy, transgene expression and associated phenotypes of the ''[[Drosophila melanogaster]]'' brain.<ref>http://www.virtualflybrain.org/</ref> Users can browse painted 3D image stacks of the ''Drosophila'' brain, choosing any plane of section they want and clicking on painted regions to find names' definitions, references and synonyms for the chosen region.  For each region, they can run queries to find neurons, [[transgene]] [[gene expression|expression]] and [[phenotype]]s.  For each neuron found, users can browse definitions, references and synonyms.
-<!-- It is a generic web-based application that allows browsing of 3D image stacks and querying of the underlying anatomy and expression database that is maintained by [http://flybase.org/ FlyBase]. The [http://www.virtualflybrain.org/site/stacks/index.htm Virtual Fly Brain] project is carried out by researchers at the [[University of Cambridge]] and the [[University of Edinburgh]]  -->
+<!-- It is a generic web-based application that allows browsing of 3D image stacks and querying of the underlying anatomy and expression database that is maintained by FlyBase<ref>http://flybase.org/ </ref>. The [http://www.virtualflybrain.org/site/stacks/index.htm Virtual Fly Brain] project is carried out by researchers at the [[University of Cambridge]] and the [[University of Edinburgh]]  -->
 ==Technical details==
-Virtual Fly Brain uses an [[Ontology (information science)|ontological model]] of ''Drosophila'' anatomy written in [http://www.w3.org/TR/owl2-primer/ OWL2] and based on the ''Drosophila'' literature. This contains detailed information about both gross neuroanatomy, neuron classes and the relationships between them<!---[[Drosophila anatomy ontology link]]-->. Underlying each neuroanatomy query is a query of this ontology in [http://www.w3.org/TR/owl2-primer/ OWL-DL].
+Virtual Fly Brain uses an [[Ontology (information science)|ontological model]] of ''Drosophila'' anatomy written in [[OWL2]] and based on the ''Drosophila'' literature. This contains detailed information about both gross neuroanatomy, neuron classes and the relationships between them<!---[[Drosophila anatomy ontology link]]-->. Underlying each neuroanatomy query is a query of this ontology in [[OWL-DL]].
-Queries of phenotype and expression utilise the large volume of expression and phenotype data in [[FlyBase]]<ref>Drysdale and FlyBase Consortium, 2008, Methods Mol. Biol. 420: 45--59</ref> annotated using the ''Drosophila'' anatomy ontology. Each expression or phenotype query starts with a query of the anatomy ontology for terms appropriate to the chosen region. The output of this query is then used as input for a query of the [[FlyBase]] [http://gmod.org/wiki/Chado_-_Getting_Started chado] database for expression or phenotype annotated using these terms.
+Queries of phenotype and expression utilise the large volume of expression and phenotype data in [[FlyBase]]<ref>{{cite journal| last=R | first=Drysdale | last2=FlyBase Consortium |  title=FlyBase : a database for the Drosophila research community|year=2008|journal= Methods Mol. Biol.|  pmid=18641940 | ref=harv | access-date=2017-06-09|doi=10.1007/978-1-59745-583-1_3|volume=420|pages= 45-59}}</ref> annotated using the ''Drosophila'' anatomy ontology. Each expression or phenotype query starts with a query of the anatomy ontology for terms appropriate to the chosen region. The output of this query is then used as input for a query of the FlyBase chado<ref>{{cite web | title=Chado - Getting Started | website=GMOD | date=13 February 2014 | url=http://gmod.org/wiki/Chado_-_Getting_Started | ref={{sfnref | GMOD | 2017}} | access-date=2017-06-09}}</ref> database for expression or phenotype annotated using these terms.
-Images in the viewer are delivered as a series of tiles covering only the visible area in the browser window. The tiles are produced from a compound 3D [http://genex.hgu.mrc.ac.uk/Software/woolz/ Woolz] object representing the overall structure and individual painted domains.
+Images in the viewer are delivered as a series of tiles covering only the visible area in the browser window. The tiles are produced from a compound 3D Woolz<ref>{{cite web | title=Woolz Image Processing: Woolz Core Software | website=EMAP Home | url=http://www.emouseatlas.org/emap/analysis_tools_resources/software/woolz/html_Core/ | ref={{sfnref | EMAP Home}} | access-date=2017-06-09}}</ref><ref>https://github.com/ma-tech/Woolz</ref> object representing the overall structure and individual painted domains.
 == References ==