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

VFB Model Context Protocol (MCP) Tool

If you used the VFB MCP tool — querying VFB through Claude or another AI assistant — please also cite the paper describing it and its evaluation:

APA

McLachlan, A. D., Court, R., Pilgrim, C., Longden, K., Brown, N. H., Osumi-Sutherland, D., Jefferis, G. S. X. E., & Armstrong, J. D. (2026). VFB-MCP: Natural-language access to Drosophila neuroscience grounded by an expert-curated ontology-led knowledgebase [Preprint]. bioRxiv. https://doi.org/10.64898/2026.06.16.732577

MLA

McLachlan, Alex D., et al. “VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase.” bioRxiv, 2026, https://doi.org/10.64898/2026.06.16.732577. Preprint.

Chicago

McLachlan, Alex D., Robert Court, Clare Pilgrim, Kit Longden, Nicolas H. Brown, David Osumi-Sutherland, Gregory S. X. E. Jefferis, and J. Douglas Armstrong. “VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase.” bioRxiv (2026). https://doi.org/10.64898/2026.06.16.732577.

BibTeX

@article{McLachlan_2026,
  author = {Alex D. McLachlan and Robert Court and Clare Pilgrim and Kit Longden and Nicolas H. Brown and David Osumi-Sutherland and Gregory S. X. E. Jefferis and J. Douglas Armstrong},
  title = "{VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase}",
  journal = {bioRxiv},
  year = {2026},
  month = {jun},
  note = {Preprint},
  doi = {10.64898/2026.06.16.732577},
  url = {https://doi.org/10.64898/2026.06.16.732577},
}

This is a preprint. If a peer-reviewed version has appeared by the time you submit, cite that instead — the DOI above will point to it.

Please cite this in addition to the primary citation, not instead of it: the MCP tool answers from the same curated knowledgebase the primary paper describes.

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

Papers citing VFB

For examples of how other groups have used Virtual Fly Brain in published work, see papers citing VFB.

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.