About Virtual Fly Brain

• 1: What is Virtual Fly Brain?
• 2: How to cite us
• 3: Privacy Notice
• 4: The Virtual Fly Brain Team
• 5: Funding
• 6: Collaborators
• 7: Contributors
• 8: Geppetto
• 9: Publications
• 10: Contact us

1 - What is Virtual Fly Brain?

Welcome to Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagents.

We integrate the neuroanatomical and expression data from the published literature, and align image datasets onto the same nervous system templates, making it possible to run cross searches, find similar neurons, and compare image data on our 3D Viewer.

2 - How to cite us

How to Cite Virtual Fly Brain

If you use Virtual Fly Brain data, tools, or resources in your research, please cite our work using the citation formats below. Proper citation helps support continued development and funding of this resource.

Primary Citation

Use this citation when referencing Virtual Fly Brain in general, including use of the website, data, or tools:

APA

Court, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., O’Kane, C. J., Armstrong, J. D., Jefferis, G. S. X. E., & Osumi-Sutherland, D. (2023). Virtual Fly Brain—An interactive atlas of the Drosophila nervous system. Frontiers in Physiology, 14. https://doi.org/10.3389/fphys.2023.1076533

MLA

Court, Robert, et al. “Virtual Fly Brain—An Interactive Atlas of the Drosophila Nervous System.” Frontiers in Physiology, vol. 14, 2023, https://doi.org/10.3389/fphys.2023.1076533.

Chicago

Court, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. “Virtual Fly Brain—An interactive atlas of the Drosophila nervous system.” Frontiers in Physiology 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.

BibTeX

@article{Court_2023,
  author = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},
  title = "{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}",
  journal = {Frontiers in Physiology},
  volume = {14},
  publisher = {Frontiers Media {SA}},
  year = {2023},
  month = {jan},
  abstract = "{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}",
  issn = {1664-042X},
  doi = {10.3389/fphys.2023.1076533},
  url = {https://doi.org/10.3389/fphys.2023.1076533},
}

Additional Citations

Drosophila Anatomy Ontology

If you specifically use or reference the Drosophila anatomy ontology developed as part of Virtual Fly Brain, please also cite:

• Osumi-Sutherland, D., Reeve, S., Mungall, C. J., Neuhaus, F., Ruttenberg, A., Jefferis, G. S. and Armstrong, J. D. (2012). A strategy for building neuroanatomy ontologies

Acknowledgements

When appropriate, please also acknowledge the specific data sources integrated into Virtual Fly Brain that you have used, such as JFRC, FlyBase, FlyCircuit, and datasets from individual research groups.

3 - Privacy Notice

Virtual Fly Brain Privacy Notice

Last updated: February 2026

The Virtual Fly Brain (VFB) project is committed to protecting your privacy and keeping you informed about how your personal information is used. This privacy notice explains how we collect, use, and protect your personal data when you visit our website.

What information do we collect?

We collect information about your visit to our website through Google Analytics, a web analytics service provided by Google, Inc. This includes:

• Your IP address (anonymized)
• Browser type and version
• Operating system
• Referring website
• Pages visited and time spent on each page
• Geographic location (country/city level only)

We do not collect any personally identifiable information such as names, email addresses, or contact details unless you voluntarily provide them (for example, through our contact forms or feedback mechanisms).

How do we use this information?

The information collected helps us:

• Understand how our website is used
• Improve the user experience and content
• Identify technical issues
• Analyze website traffic patterns
• Support our research by understanding user interests in neuroanatomical data

Cookies and Website Privacy

We use Google Analytics cookies to collect this information. These are small text files stored on your device. You can control cookies through your browser settings, and you can opt out of Google Analytics tracking by visiting Google Analytics Opt-out.

For more information about Google’s privacy practices, please see Google’s Privacy Policy.

Legal Basis for Processing

Our processing of your personal data is based on:

• Legitimate interests: To improve our website and research services
• Consent: Where you have provided it for specific purposes

Data Sharing and Disclosure

We do not sell, rent, or trade your personal information. Information collected by Google Analytics may be processed by Google on servers located in the United States. Google is committed to complying with the EU-U.S. Privacy Shield framework.

Data Retention

Analytics data is retained for up to 26 months, after which it is automatically deleted.

Your Rights

Under data protection law, you have rights including:

• Access: Request a copy of your personal data
• Rectification: Correct inaccurate data
• Erasure: Request deletion of your data
• Restriction: Limit how we process your data
• Objection: Object to processing based on legitimate interests
• Portability: Receive your data in a structured format

Contact Us

If you have questions about this privacy notice or wish to exercise your rights, please contact:

Data Protection Officer
University of Edinburgh
Old College
South Bridge
Edinburgh EH8 9YL
Email: dpo@ed.ac.uk

VFB Project Team
Email: data@virtualflybrain.org

Changes to this Privacy Notice

We may update this privacy notice from time to time. Any changes will be posted on this page with an updated revision date.

This privacy notice is supported by the University of Edinburgh’s wider privacy policies. For more information, visit the University Data Protection webpages.

4 - The Virtual Fly Brain Team

Current Team Members

• Robert Court (Lead DevOps) [1]

• Clare Pilgrim (Ontology Editor/Curator) [2]

• Alex McLachlan (Curator/UX Tester) [2]

• Gillian Millburn (Senior Curator) [2]

• Douglas Armstrong (Current Project PI) [1]

• Nick Brown (Current Project PI) [2]

• Greg Jefferis (Current Project PI) [4,5]

• David Osumi-Sutherland (Current Project Co-I) [3]

• Marta Costa (Current Project Co-I) [4]

Past Team Members

• Nestor Milyaev (2009-2012) [1]

• Alex Holmes (2017-2019) [2]

• Aoife Larkin (2017-2019) [2]

• Huseyin Kir (2021-2024) [6]

• Nico Matentzoglu (2018-2022) [6]

• Simon Reeve (2009-2011) [7]

• Nicole Staudt (2015-2016) [7]

• Helen Parkinson (Former PI) [6]

• Cahir O’Kane (Former PI) [7]

• Michael Ashburner (Original PI and Grant Holder) [7]

Affiliations

1. Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh
2. Department of Physiology, Development and Neuroscience
3. Wellcome Sanger Institute, Cambridge
4. Department of Zoology, University of Cambridge
5. MRC Laboratory of Molecular Biology, Cambridge
6. European Bioinformatics Institute (EMBL-EBI), Cambridge
7. Department of Genetics, University of Cambridge

MetaCell

MetaCell collaborates with Virtual Fly Brain on the development and enhancement of the open source Geppetto visualization platform that powers our 3D brain viewer.

For questions about team members or collaboration opportunities, please contact us.

5 - Funding

Current Funding (2022-2027)

Wellcome Trust Grant 223741/Z/21/Z

• Duration: April 1, 2022 to March 31, 2026 (extended to March 31, 2027)
• Supporting ongoing Virtual Fly Brain development and maintenance

Historical Funding

Wellcome Trust

Grant 208379/Z/17/Z

• Duration: October 1, 2017 to October 1, 2021

“Virtual Fly Brain: a global informatics hub for Drosophila neurobiology”

• Grant 105023/D/14/Z: October 1, 2014 to January 31, 2018
• Grant 105023/A/14/Z: October 1, 2014 to January 31, 2018
• Grant 105023/C/14/Z: October 1, 2014 to September 30, 2017
• Grant 105023/B/14/Z: October 1, 2014 to September 30, 2017

UK Research Councils

Biotechnology and Biological Sciences Research Council (BBSRC)

• Grant BB/G02233X/1 (2009): “Standardising the representation of Drosophila anatomy and development for databases”
• Recipients: J. Douglas Armstrong, Michael Ashburner, Cahir O’Kane, David Osumi-Sutherland

Engineering and Physical Sciences Research Council (EPSRC)

• UK e-Science Theme Award supporting initial project establishment
• Recipient: J. Douglas Armstrong

Medical Research Council (MRC)

• Ongoing institutional support for technical infrastructure development

Other Sources

Isaac Newton Trust (University of Cambridge)

• Grant supporting David Osumi-Sutherland’s database work (2007)
• Grant supporting Marta Costa’s research: “Neuroinformatic identification of new types of neuron in the Drosophila brain” (October 2012 - September 2013)

Wellcome Trust - Cambridge Protein Trap Project

• Supporting BrainTrap database development
• Recipients: Kathryn Lilley, Steve Russell, Daniel St. Johnson

Institutional Partners

Virtual Fly Brain is a collaborative project between:

• University of Edinburgh - School of Informatics
• University of Cambridge - Departments of Physiology Development & Neuroscience, and Zoology
• Wellcome Sanger Institute - Hinxton, UK
• MRC Laboratory for Molecular Biology - Cambridge

Data Partnerships

Virtual Fly Brain integrates data from multiple sources through collaborative partnerships rather than direct funding arrangements:

• FlyBase Consortium
• FlyCircuit Project (National Tsing Hua University, Taiwan)
• Janelia Research Campus (HHMI, USA)
• Multiple international research laboratories

Site Visualization Tools

Virtual Fly Brain utilizes multiple visualization technologies:

Geppetto Framework

• Open source 3D visualization platform co-developed with MetaCell Corporation
• VirtualFlyBrain and MetaCell collaborate on ongoing development and improvements to the Geppetto ecosystem

Woolz Image Processing and IIP3D Server

• Developed by the MRC Human Genetics Unit, University of Edinburgh
• Provides high-performance image serving and client-side visualization tools

6 - Collaborators

Collaborators

The IIP3D server, Woolz software and client-side tools are developed by* MRC Human Genetics Unit (MRC HGU): Richard Baldock, Nick Burton, Bill Hill, Zsolt Husz
(*) An on-going development of the client-side tools is done in collaboration between the MRC HGU and Edinburgh University

Visit the EMAGE gene expression database to see other tools the MRC HGU have developed.

Expression data is collaboratively curated by VFB and FlyBase and stored and maintained at FlyBase.

Phenotype data is curated, stored, and maintained by FlyBase.

7 - Contributors

Contributors

We would like to thank the following contributors for their help with this project:

8 - Geppetto

Geppetto is an open source project that VFB is an active developer of in partnership with MetaCell

For full details on the project see Geppetto.org

Geppetto

Build robust neuroscience applications.

| Live demo | Paper | Docs |

The visualisation and simulation platform focused on what matters to you.

Neuroscience software reimagined

Geppetto is a web-based visualisation and simulation platform to build neuroscience software applications. Reuse best practices, best compomnents, best design. Don’t reinvent the wheel.

A completely modular platform.

Engineered together with scientists, Geppetto lets you integrate different data and models. A modular architecture allows the platform to easily support different standard formats for both experimental and computational data.

An open-source revolution.

Geppetto is entirely open source and engineers, scientists and developers from different research groups are contributing to its development by adding functionality to visualize and simulate new data and models.

Awesome in-browser 3D

Geppetto enables visualizing and interacting with 3D data in your web browser. Take advantage of out of the box support for point clouds, ball-and-stick models, line segments for large networks or arbitrarly complex meshes.

Extensible components based framework

A modular system of components allows both experimental and simulated data to be visualized in domain specific ways so that you can always be in control of how to present your data.

Fully indexed and searchable data and models

The data and models loaded inside Geppetto are fully indexed and searchable for you to always find what is most important without big data getting in the way.

Dynamic visualisation

We know you are used to look at your simulations only via a plot or a static rendered video. In Geppetto the 3D models can be linked to your simulation to add a dynamic visual component to your computational experiments.

A powerful abstraction

Geppetto defines a model abstraction capable of representing different classes of models and data, in a generic way. In this way the platform can be used over and over by different groups, becoming more and more robust, generic and smart.

Features

Some of the features responsible for giving you an amazing experience.

Regular releases of Geppetto make sure components keep being updated and tested.

Help us identify what matters to you and what you would want to see built in Geppetto. Do so by logging an enhancement request on GitHub or dropping us an email.

Curious to know more about Geppetto?

Gallery

Some screenshots of what is possible today. Imagine the future.

Get involved!

Help us build the next generation simulation platform!

Geppetto is entirely open source and is being built by a growing community of talented engineers and scientists. Geppetto uses different languages to achieve different goals. Geppetto runs on the Eclipse Virgo WebServer and can be deployed on different infrastructures including cloud-based ones like Amazon EC2.

Geppetto is multi-platform and works on Linux, Mac OSX and Windows, so no matter on what platform you develop there is a way for you to run it and add fantastic contributions.

Show me the code!

Right! Geppetto is hosted on GitHub, every module has its own repository to provide flexible ways of branching individual components. For every module we have at least two branches, development and master. The development branch gets merged into master each monthly release. If you want to contribute you can either go straight to the code or reach out to us dropping an email, we will show you around and help you contribute in your favorite way!

| Source code | Docs | Development board

F.A.Q.

Find some answers to the most common questions about Geppetto!

Who is building Geppetto?

Many engineers and scientists contribute every day to the development of Geppetto, a big thank to our superheroes:

• Matteo Cantarelli (Coordinator, principal architect, engineer)
• Giovanni Idili (Architect, engineer)
• Afonso Pinto (Engineer)
• Adrian Quintana Perez (Architect, engineer)
• Boris Marin (Architect, computational scientist)
• Dario Del Piano (Engineer)
• Facundo Rodriguez (Engineer)
• Filippo Ledda (Architect, engineer)
• Jesus Martinez (Engineer)

For the full list of contributors see here.

Why are you building Geppetto?

Read our paper to learn more.

Besides the functional requirements, Geppetto’s goal is to move away from the monolithic approach to software that is usually found in academic programming projects.

Computational neuroscience has produced software systems, including NEURON and Genesis, that are extremely useful for simulating systems of neurons that include biophysical details (Brette et al, 2007). A range of other algorithms have been devised in other areas of computational biology (Barnes & Chu, 2010) for which simulators have been produced (Takahashi, 2004). Several investigations have pointed to the challenges in building a single system that integrates multiple simulation algorithms together into a single biological model (Takahashi et al., 2002, Dada and Mendes, 2007, Cornelis et al., 2012).

Geppetto aims to address these scientific and engineering challenges. Geppetto’s design leverages cutting edge software technologies. Its architecture and development follows industry standards.

How is Geppetto development funded?

Building great software takes time. And money. Geppetto is no exception and as many open-source projects it is funded by a hybrid model. Geppetto’s development is supported by both awesome volunteer contributors and by external companies and organisations:

• OpenWorm
• MetaCell
• Wellcome Trust via the Open Source Brain initiative
• Wellcome Trust via Virtual Fly Brain
• Orion Bionetworks

Commercial companies, academic institutions and independent research labs are welcome to get in touch with us to discuss collaborations and grant applications.

What is Geppetto’s relationship with OpenWorm?

The decision to build Geppetto came after an analysis of the requirements for a platform able to support the OpenWorm full-scale simulation of the C. elegans.

Geppetto’s architecture is generic and therefore the simulation of the C.elegans is just one specific simulation it is capable of. Geppetto’s modules can be built to simulate and integrate any complex system.

What license does Gepetto have?

Geppetto is released under the MIT license.

Arr, didn’t find what you were looking for? Check out our docs

9 - Publications

Publications

For more information on the technology behind the VFB website:

• Robert Court, Marta Costa, Clare Pilgrim, Gillian Millburn, Alex Holmes, Alex McLachlan, Aoife Larkin, Nicolas Matentzoglu, Huseyin Kir, Helen Parkinson, Nicolas H. Brown, Cahir J. O’Kane, J. Douglas Armstrong, Gregory S. X. E. Jefferis and David Osumi-Sutherland (2023). Virtual Fly Brain - An interactive atlas of the Drosophila nervous system. Frontiers in Physiology 14.
• Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Robert Court, Padraig Gleeson, Salvador Dura-Bernal, R. Angus Silver, Giovanni Idili (2018). Geppetto: a reusable modular open platform for exploring neuroscience data and models. Philosophical Transactions of the Royal Society B: Biological Sciences 373.
• Hilmar Lapp, James P. Balhoff, Todd J. Vision (2017). Owlery: A flexible approach for the serving of OWL ontologies. bioRxiv.
• Milyaev, N., Osumi-Sutherland, D., Reeve, S., Burton, N., Baldock, R. A. and Armstrong, J. D. (2012). The Virtual Fly Brain browser and query interface. Bioinformatics 28, 411-5.
• Husz ZL, Burton N, Hill B, Milyaev N, Baldock RA:Web tools for large-scale 3D biological images and atlases. BMC Bioinformatics 13:122, 2012.

For details on the anatomy ontology:

• Osumi-Sutherland, D., Reeve, S., Mungall, C. J., Neuhaus, F., Ruttenberg, A., Jefferis, G. S. and Armstrong, J. D. (2012). A strategy for building neuroanatomy ontologies. Bioinformatics 28, 1262-1269.

10 - Contact us

Contact Virtual Fly Brain

We welcome feedback, questions, and collaboration opportunities from the Drosophila research community. Please choose the most appropriate contact method for your inquiry below.

Technical Support & General Questions

For help with using Virtual Fly Brain, comments, suggestions, or general questions:

Public Support Forum: support@virtualflybrain.org

Note: This email goes to our public support forum, where questions and responses are visible to the community, helping other users with similar issues.

Before emailing: Please check our support forum archives to see if your question has already been answered.

Bug Reports & Feature Requests

To report technical issues, bugs, or request new features:

GitHub Issues: Report an issue

This allows our development team to track and address technical problems efficiently.

Data Contributions & Private Inquiries

For data inclusion discussions, collaboration proposals, or confidential matters that require direct communication with our team:

Private Email: data@virtualflybrain.org

Learn more about data contributions: Contribution Guidelines

Collaboration & Partnerships

Interested in collaborating with the Virtual Fly Brain team or discussing partnership opportunities?

Contact: data@virtualflybrain.org

Questions about Data Inclusion

For questions about adding your data:

Contact: data@virtualflybrain.org

Stay Connected

• BlueSky: Follow us for updates and announcements
• LinkedIn: Follow us for updates and announcements
• GitHub: VirtualFlyBrain organization - contribute to our open source development