# Virtual Fly Brain

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frame|alt=VFB logo|Virtual Fly Brain icon
'''Virtual Fly Brain''', or '''VFB''', is an interactive, web-based tool that allows [neurobiologist](/source/neurobiologist)s to explore the detailed [neuroanatomy](/source/neuroanatomy), [transgene](/source/transgene) [expression](/source/gene_expression) and associated [phenotype](/source/phenotype)s of the ''[Drosophila melanogaster](/source/Drosophila_melanogaster)'' brain.<ref>{{Cite web|url=https://www.virtualflybrain.org/|title=Virtual Fly Brain|website=Virtual Fly Brain}}</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 [neuron](/source/neuron)s, transgene expression and phenotypes.  For each neuron found, users can browse definitions, references and synonyms.

==Background==
Virtual Fly Brain 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>{{cite web| url=http://flybase.org/ | title=FlyBase Homepage - A Database of Drosophila Genes & Genomes | access-date=2023-12-23}}</ref> The [https://www.virtualflybrain.org/ Virtual Fly Brain] project is carried out by researchers at the [University of Cambridge](/source/University_of_Cambridge) and the [University of Edinburgh](/source/University_of_Edinburgh).

==Technical details==
Virtual Fly Brain uses an [ontological model](/source/Ontology_(information_science)) of ''Drosophila'' anatomy written in [OWL2](/source/Web_Ontology_Language) 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](/source/Drosophila_anatomy_ontology_link)-->. Underlying each neuroanatomy query is a query of this ontology in [OWL-DL](/source/OWL-DL).

Queries of phenotype and expression utilise the large volume of expression and phenotype data in [FlyBase](/source/FlyBase)<ref>{{cite book| last1=R | first1=Drysdale | last2=FlyBase Consortium | title=Drosophila | chapter=FlyBase: A Database for the Drosophila Research Community |year=2008|series= Methods Mol. Biol.|  pmid=18641940 |doi=10.1007/978-1-59745-583-1_3|volume=420|pages= 45–59| isbn=978-1-58829-817-1 }}</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 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>{{Cite web|url=https://github.com/ma-tech/Woolz|title = Ma-tech/Woolz|website = [GitHub](/source/GitHub)|date = 10 May 2021}}</ref> object representing the overall structure and individual painted domains.

==See also==
*[Insect brain](/source/Insect_brain)
*[Drosophila connectome](/source/Drosophila_connectome)
*[Ganglion mother cell](/source/Ganglion_mother_cell)
*[Pigment dispersing factor](/source/Pigment_dispersing_factor)

== References ==
{{Reflist}}

== External links ==
* [http://www.virtualflybrain.org/site/stacks/index.htm virtualflybrain.org] {{Webarchive|url=https://web.archive.org/web/20110728162121/http://www.virtualflybrain.org/site/stacks/index.htm |date=2011-07-28 }}
* [http://flybase.org/ FlyBase]

<!--- Categories --->
Category:Neuroanatomy
Category:Drosophila melanogaster
Category:Invertebrate nervous system

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Adapted from the Wikipedia article [Virtual Fly Brain](https://en.wikipedia.org/wiki/Virtual_Fly_Brain) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Virtual_Fly_Brain?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.