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About 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. 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, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons and compare image data on our 3D Viewer.

1: How to cite us
2: What is Virtual Fly Brain?
3: Virtual Fly Brain Members and Their Contributions
4: Collaborators
5: Contributors
6: Publications
7: VFB citation bibtex
8: Contact us

1 - How to cite us

Please use the citation below:

APA

Court, R., Costa, M., Pilgrim, C., Millburn, G., Holmes, A., McLachlan, A., Larkin, A., Matentzoglu, N., Kir, H., Parkinson, H., Brown, N. H., J., C., Armstrong, J. D., & Jefferis, G. S. (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{10.3389/fphys.2023.1076533,
  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},
}

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](http://dx.doi.org/doi:10.1093/bioinformatics/bts113

2 - What is Virtual Fly Brain?

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

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, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons, and compare image data on our 3D Viewer.

3 - Virtual Fly Brain Members and Their Contributions

Who We Are

3D Viewer, Online Tools, Server, and Website

Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh

Robert Court (Lead DevOps)
Douglas Armstrong (current project PI)
Nestor Milyaev (2009-2012)

Ontology Editing, FlyBase Support, and Data Annotation

Department of Genetics, University of Cambridge

Cahir O’Kane (current project PI)
Michael Ashburner (original PI and grant holder)
Simon Reeve (2009-2011)
Nicole Staudt (2015-2016)
Alex Holmes (2017-2019)

Department of Physiology, Development and Neuroscience

Clare Pilgrim (Ontology editor/Curator)
Alex McLachlan (Curator/UX Tester)
Aoife Larkin (Curator)
Gillian Millburn (Senior Curator)
Nick Brown (current project PI)

Department of Zoology, University of Cambridge

Marta Costa (current project Co-I)

Image Processing, Registration, and NBLAST Neuron Search

MRC Laboratory of Molecular Biology, Cambridge

Greg Jefferis (current project PI)

Schema Development & Web Development

European Bioinformatics Institute (EMBL-EBI), Cambridge

David Osumi-Sutherland (current project Co-I)
Huseyin Kir (developer)
Nico Matentzoglu (developer)
Helen Parkinson (current project PI)

Software engineering, Geppetto customisation, graphics design

MetaCell

4 - 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. Phenotype data is curated by FlyBase. Expression and phenotype data displayed on VFB is stored and maintained by FlyBase.

5 - Contributors

A list of contributors to the VirtualFlyBrain project

Contributors

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

6 - 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.
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.

7 - VFB citation bibtex

@article{Court_2023, 
    doi = {10.3389/fphys.2023.1076533}, 
    url = {https://doi.org/10.3389%2Ffphys.2023.1076533}, 
    year = 2023, 
    month = {jan}, 
    publisher = {Frontiers Media {SA}}, 
    volume = {14}, 
    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{\textemdash}An interactive atlas of the Drosophila nervous system}, journal = {Frontiers in Physiology}}

8 - Contact us

To report a bug on the site, use the Report an issue help menu link. For help, comments or suggestions, please use support@virtualflybrain.org.

To tell us about new data that you generated that could be incorporated into VFB see here.

Using our software or registered image data

The VFB software can be embedded in any third-party website where it can provide the same functionality as on the VFB website. This is because it was developed as part of an open source project and freely distributed under a GNU GPL2 license.

If you use our registered image stacks in any publication, please cite the original authors (see Source for each image) and the VFB project.