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University of Edinburgh, MRC Laboratory of Molecular Biology, European Bioinformatics Institute

University of Edinburgh, MRC Laboratory of Molecular Biology, European Bioinformatics Institute

Virtual Fly Brain

Virtual Fly Brain (VFB) is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster.

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What is Virtual Fly Brain?

Virtual Fly Brain (http://virtualflybrain.org) is a joint effort of University of Edinburgh, LMB Cambridge and EBI, funded by the Wellcome Trust, to produce fly brain data-driven imaging, visualization and browsing. Using a 3D Brain Viewer, it is possible to explore the fruit fly anatomy, as well as view image stacks from datasets integrated by Virtual Fly Brain.

What did MetaCell do for Virtual Fly Brain?

MetaCell built Virtual Fly Brain 2.0. The team first assessed the requirements and user stories for a functional specification to build the new version of the site then built and coordinated the construction of a new integrated 2D and 3D data browser for drosophila data. The project lasted one year.

The team implemented Virtual Fly Brain 2.0 using Geppetto (http://geppetto.org), an open source visualization and simulation platform that MetaCell has contributed to since its creation in 2013. As Geppetto already enabled many desirable features needed by the Virtual Fly Brain browser, MetaCell was able to successfully flesh out only the functionality that needed development, reducing costs and time to delivery of the project, and maximising outcome.

What functionality did MetaCell implement?

  • Explore / query Virtual Fly Brain data
  • Fetch 2D and 3D data in real time
  • Visualize expression patterns as point cloud data
  • Visualize segmented neurons, neuropil, expression patterns and 2D stacks
  • Connect to Neo4j and AberOWL Virtual Fly Brain knowledge base data sources
  • And much more...

What's the result?

An interactive online tool – Virtual Fly Brain 2.0 – was built for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. By integrating data from published literature and image datasets, Virtual Fly Brain 2.0 makes it possible to run cross searches, explore the available data sets and images for the Drosophila melanogaster without the user ever having to leave the web browser.

What can I do with Virtual Fly Brain?

  • Explore the Drosophila melanogaster brain from any web browser
  • Visualise 2D and 3D fly data
  • Visualise expression patterns as point clouds
  • Use data loaded from the web browser in real time and add it to the brain on demand
  • Search for anything inside the brain and run queries to explore it in depth
  • Add any data set to the brain with a simple click - and customise it
  • Access data from a seamlessly integrated ontology knowledge base
"We are delighted to have found in MetaCell a developer with a very high level of professionalism, people who understand science and who are committed to the open source model. Their work has combined architectural rigour and good development practice with a healthy dose of visual flair. We certainly intend to work with them again."
Testimonial person picture
Gregory Jefferis
Group Leader at MRC Laboratory of Molecular Biology, Cambridge
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About the CLIENT

Academia

Date

January 2020

Virtual Fly Brain in a nutshell.

  • Explore the Drosophila melanogaster brain from any web browser
  • Visualise 2D and 3D fly data
  • Visualise expression patterns as point clouds
  • Use data loaded from the web browser in real time and add it to the brain on demand
  • Search for anything inside the brain and run queries to explore it in depth
  • Add any data set to the brain with a simple click - and customise it
  • Access data from a seamlessly integrated ontology knowledge base
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Key results
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Requirements
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User Stories
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