This is the multi-page printable view of this section. Click here to print.
About Virtual Fly Brain
- 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
- 9: Archived sites hosted by Virtual Fly Brain
- 9.1: BrainTrap
- 9.2: FAFB CATMAID Data Viewer
- 9.3: FANC CATMAID Data Viewer
- 9.4: FLYBRAIN Neuron Database (NDB)
- 9.5: IAV-TNT CATMAID Data Viewer
- 9.6: L1EM CATMAID Data Viewer
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., 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{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 = {https://doi.org/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
2 - 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, 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
![](https://v2.virtualflybrain.org/images/vfb/project/logos/InformaticsLogo.gif)
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
![](https://v2.virtualflybrain.org/images/vfb/project/logos/CUnibig.png)
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
![](https://v2.virtualflybrain.org/images/vfb/project/logos/MRC-LMB_logo.png)
MRC Laboratory of Molecular Biology, Cambridge
- Greg Jefferis (current project PI)
Schema Development & Web Development
Wellcome Sanger Institute, Cambridge
- David Osumi-Sutherland (current project Co-I)
![](https://v2.virtualflybrain.org/images/vfb/project/logos/EMBL_EBI_logo_180pixels_RGB.png)
European Bioinformatics Institute (EMBL-EBI), Cambridge
- Huseyin Kir (developer)
- Nico Matentzoglu (developer)
- Helen Parkinson (current project PI)
Software engineering, Geppetto customisation, graphics design
![](https://github.com/tarelli/bucket/raw/master/MetaCellLogoWhite300ppi.png)
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
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/fphys.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.
9 - Archived sites hosted by Virtual Fly Brain
9.1 - BrainTrap
https://braintrap.virtualflybrain.org/
Overview
BrainTrap was developed as part of a large-scale collaborative research project to collect protein expression location information from protein-trap lines generated by the Cambridge Protein Trap (CPT) project. The database provides detailed 3D confocal datasets showing protein expression patterns throughout the adult Drosophila brain.
Features
- Interactive web-based viewer for exploring 3D confocal datasets
- Full-size images throughout the brain volume can be viewed interactively
- Secondary immunohistochemical label (anti-brp) aids navigation and helps identify brain structures
- Searchable annotations linked to the FlyBase Drosophila anatomy ontology
- Anatomical search criteria can be specified using:
- Automatic term completion
- Hierarchical browser for the ontology
- Annotation provenance tracking with highlighted expression locations
- Downloadable confocal dataset files in original format
- XML format annotation data export
- Gene comparison tables for selected genes
Original Publication
Knowles-Barley S, Longair M and Armstrong JD (2010). BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database, Vol. 2010, Article ID baq005, doi:10.1093/database/baq005 (https://doi.org/10.1093/database/baq005)
Funding
Original development was funded by:
- Engineering and Physical Sciences Research Council (EPSRC)
- Medical Research Council
- Biotechnology and Biological Sciences Research Council (BBSRC)
- British Society for Developmental Biology
- Society for Experimental Biology
- Virtual Fly Brain e-Science Institute (ESI) Theme
The fly lines were generated by the Cambridge Protein Trap Project, supported by a Wellcome Trust grant to Kathryn Lilley, Steve Russell and Daniel St. Johnson.
Current Maintenance
This resource is currently archived and maintained by Virtual Fly Brain (VFB).
Current website: https://braintrap.virtualflybrain.org/
Source code repository: https://github.com/VirtualFlyBrain/BrainTrap
Original Development
School of Informatics
The University of Edinburgh
Edinburgh, EH8 9AB, UK
Citation
If you use BrainTrap in your research, please cite:
Knowles-Barley S, Longair M and Armstrong JD (2010). BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database, Vol. 2010, Article ID baq005, doi:10.1093/database/baq005 (https://doi.org/10.1093/database/baq005)
9.2 - FAFB CATMAID Data Viewer
Access
The FAFB CATMAID instance is hosted and maintained by Virtual Fly Brain (VFB) as part of their mission to integrate and preserve key Drosophila neuroscience datasets. The instance is accessible at: https://fafb.catmaid.virtualflybrain.org/
This resource provides access to the FAFB dataset and its associated neural reconstructions. Virtual Fly Brain ensures its long-term availability to the research community.
Source Publications
Primary Resources
- FAFB Project: https://www.zoo.cam.ac.uk/research/groups/connectomics
- EM Dataset: Zheng Z, et al. (2018) A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell, 174(3), 730-743.e22. https://doi.org/10.1016/j.cell.2018.06.019
Contributing Publications
The database includes neurons traced and published in numerous studies. Each neuron is annotated with its source publication. Major contributing publications include:
- Baltruschat et al. (2021)
- Bates and Schlegel et al. (2020)
- Coates et al. (2020)
- Dolan and Belliart-Guérin et al. (2018)
- Dolan et al. (2019)
- Engert et al. (2022)
- Felsenberg et al. (2018)
- Gorko et al. (2024)
- Hampel and Eichler et al. (2020)
- Kim et al. (2020)
- Kind et al. (2021)
- Marin et al. (2020)
- Morimoto et al. (2020)
- Otto et al. (2020)
- Sayin et al. (2019)
- Shiu et al. (2022)
- Taisz and Galili et al. (2022)
- Turner-Evans et al. (2020)
- Wang et al. (2020a, 2020b, 2020c)
- Zhao et al. (2023)
- Zheng et al. (2018, 2022)
Full references for specific neurons can be found on Virtual Fly Brain by searching for their skeleton ID (skid).
Dataset Contents
The viewer provides access to:
- Complete electron microscopy volume of an adult Drosophila melanogaster brain
- Manually traced neuron reconstructions from multiple research groups
- Synaptic connectivity information
- Associated metadata and annotations
Features
This CATMAID instance enables:
- Browser-based visualization of the serial section electron microscopy data
- Navigation through image stacks
- Viewing of neuron reconstructions
- Analysis of synaptic connectivity
- Data export functionality
Available Tools
- Tracing tool for examining reconstructions
- Neuron search interface with paper-based filtering
- Connectivity analysis tools
- Skeleton visualization options
- API access for programmatic data retrieval (documentation: https://catmaid.readthedocs.io/en/stable/api.html): https://fafb.catmaid.virtualflybrain.org/apis/
Citation Guidelines
When using this data, please cite:
-
The FAFB EM dataset: Zheng Z, et al. (2018) A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell, 174(3), 730-743.e22. https://doi.org/10.1016/j.cell.2018.06.019
-
The CATMAID platform: Saalfeld S, Cardona A, Hartenstein V, Tomančák P (2009) CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25(15): 1984-1986. https://doi.org/10.1093/bioinformatics/btp266
-
The specific publication(s) associated with any neurons you analyze or reference (see Contributing Publications section)
Maintenance & Support
This resource is archived, hosted, and maintained by Virtual Fly Brain (VFB - https://virtualflybrain.org) as part of their commitment to preserving and making accessible critical Drosophila neuroscience data resources.
9.3 - FANC CATMAID Data Viewer
Access
The FANC CATMAID instance is hosted and maintained by Virtual Fly Brain (VFB) as part of their mission to integrate and preserve key Drosophila neuroscience datasets. The instance provides two views of the data:
-
Original EM stack and tracings (Project ID 1): https://fanc.catmaid.virtualflybrain.org/
-
Neurons aligned to JRC2018 VNC female template (Project ID 2): https://fanc.catmaid.virtualflybrain.org/
This resource provides access to both the original FANC dataset and template-aligned reconstructions. Virtual Fly Brain ensures its long-term availability to the research community.
Source Publication
The data is from the research published in:
Fushiki A, et al. (2021) A circuit mechanism for the propagation of waves of muscle contraction in Drosophila. Cell, 184(3), 759-774.e20. https://doi.org/10.1016/j.cell.2020.12.013
see: https://www.lee.hms.harvard.edu/resources
Dataset Contents
The viewer provides access to:
- Complete electron microscopy volume of an adult female Drosophila ventral nerve cord
- Manually traced neuron reconstructions in original EM space
- Template-aligned neurons in JRC2018 VNC female template space
- Synaptic connectivity information
- Associated metadata and annotations
Features
This CATMAID instance enables:
- Browser-based visualization of the serial section electron microscopy data
- Navigation through image stacks
- Viewing of neuron reconstructions in both original and template space
- Analysis of synaptic connectivity
- Data export functionality
Available Tools
- Tracing tool for examining reconstructions
- Neuron search interface
- Connectivity analysis tools
- Skeleton visualization options
- API access for programmatic data retrieval (documentation: https://catmaid.readthedocs.io/en/stable/api.html): https://fanc.catmaid.virtualflybrain.org/apis/
Note: Both views (original and aligned) can be accessed through the same API using different project IDs (pid).
Citation Guidelines
When using this data, please cite:
-
The FANC dataset: Fushiki A, et al. (2021) A circuit mechanism for the propagation of waves of muscle contraction in Drosophila. Cell, 184(3), 759-774.e20. https://doi.org/10.1016/j.cell.2020.12.013
-
The CATMAID platform: Saalfeld S, Cardona A, Hartenstein V, Tomančák P (2009) CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25(15): 1984-1986. https://doi.org/10.1093/bioinformatics/btp266
Maintenance & Support
This resource is archived, hosted, and maintained by Virtual Fly Brain (VFB - https://virtualflybrain.org) as part of their commitment to preserving and making accessible critical Drosophila neuroscience data resources. The aligned neurons are also available through the Virtual Fly Brain website.
9.4 - FLYBRAIN Neuron Database (NDB)
https://flybrain-ndb.virtualflybrain.org/
Database Structure
FLYBRAIN NDB is a relational database searchable by two main criteria:
1. Neuron Search
Search neurons by:
- Name (full or partial)
- Areas of arborizations
- Distribution of pre- or postsynaptic sites (where known)
- Keywords in documentation
2. Strain/Antibody Search
Search molecular markers including:
- Antibodies
- Drosophila strains (e.g., GAL4 enhancer-trap lines)
- Specific neural pathways
Data Categories
- Visual Neurons
- Olfactory Neurons
- Auditory Neurons
- Gustatory Neurons
- Central Complex Neurons
- Clonal Units
- Brain Region Definitions
- GAL4 and LexAV Strain Collections
Brain Explorer Features
The online brain browsing system allows users to:
- Rotate volume-rendered images
- Create sections
- Adjust magnification
- Browse confocal data
Terms of Use
Access
- FLYBRAIN NDB is freely available
- No login or registration required
Copyright
- All contents © 2008 FLYBRAIN NDB or their original publication
- Copyright is noted in respective images
Usage Rights
- Free use for non-profit, educational, and scientific purposes with proper citation
- Republication or commercial use requires consent from the FLYBRAIN NDB manager
Citation Guidelines
Citing the Database
When citing the database as a whole, use: “Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org)”
Citing Specific Records
Format: [Neuron type], [Author(s)], ([Year]) Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org), acc. [number]
Example: “LC10 neuron, Otsuna, H., and Ito, K. (2007) Flybrain Neuron Database (https://flybrain-ndb.VirtualFlyBrain.org), acc. 10010”
Important Notes:
- Include accession numbers when citing specific neurons
- Cite original publications where applicable
- Multiple contributors may exist for each record
Current Maintenance
This resource is currently archived and maintained by Virtual Fly Brain (VFB).
Source code repository: https://github.com/VirtualFlyBrain/flybrain-ndb
Original Development
© 2010 FLYBRAIN Neuron Database
Original Contact: Kazunori Shinomiya
9.5 - IAV-TNT CATMAID Data Viewer
Access
The IAV-TNT CATMAID instance is hosted and maintained by Virtual Fly Brain (VFB) as part of their mission to integrate and preserve key Drosophila neuroscience datasets. The instance is accessible at: https://iav-tnt.catmaid.virtualflybrain.org/
This resource provides a direct view into the dataset used to study the organization of proprioceptive circuits in Drosophila larvae. Virtual Fly Brain ensures its long-term availability to the research community.
Source Publication
This data is from the research published in:
Valdes-Aleman J, et al. (2021). Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in the Drosophila Motor System. Neuron, 109(1), 105-120.e7. https://doi.org/10.1016/j.neuron.2020.10.004
Dataset Contents
The viewer provides access to:
- Serial section electron microscopy data of Drosophila larval segments
- Reconstructions of IAV sensory neurons
- Synaptic connectivity information
- Associated metadata and annotations
Features
This CATMAID instance enables:
- Browser-based visualization of the serial section electron microscopy data
- Navigation through image stacks
- Viewing of neuron reconstructions
- Analysis of synaptic connectivity
- Data export functionality
Available Tools
- Tracing tool for examining reconstructions
- Neuron search interface
- Connectivity analysis tools
- Skeleton visualization options
- API access for programmatic data retrieval (documentation: https://catmaid.readthedocs.io/en/stable/api.html): https://iav-tnt.catmaid.virtualflybrain.org/apis/
Citation Guidelines
When using this data, please cite both:
-
The original research: Valdes-Aleman J, et al. (2021). Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in the Drosophila Motor System. Neuron, 109(1), 105-120.e7. https://doi.org/10.1016/j.neuron.2020.10.004
-
The CATMAID platform: Saalfeld S, Cardona A, Hartenstein V, Tomančák P (2009) CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25(15): 1984-1986. https://doi.org/10.1093/bioinformatics/btp266
Maintenance & Support
This resource is archived, hosted, and maintained by Virtual Fly Brain (VFB - https://virtualflybrain.org) as part of their commitment to preserving and making accessible critical Drosophila neuroscience data resources.
9.6 - L1EM CATMAID Data Viewer
Access
The L1EM CATMAID instance is hosted and maintained by Virtual Fly Brain (VFB) as part of their mission to integrate and preserve key Drosophila neuroscience datasets. The instance is accessible at: https://l1em.catmaid.virtualflybrain.org/
This resource provides access to the L1EM dataset and its associated neural reconstructions. Virtual Fly Brain ensures its long-term availability to the research community.
Source Publication
Primary Resource
- L1EM Dataset: Winding M, et al. (2023) The connectome of an insect brain. Science, 379(6636):eadd9330. https://doi.org/10.1126/science.add9330
Contributing Publications
The database includes neurons traced and published in numerous studies. Each neuron is annotated with its source publication. Major contributing publications include:
- Andrade et al. (2019)
- Barnes et al. (2022)
- Berck, Khandelwal et al. (2016)
- Burgos et al. (2018)
- Carreira-Rosario, Arzan Zarin, Clark et al. (2018)
- Eichler, Li, Litwin-Kumar et al. (2017)
- Eschbach, Fushiki et al. (2020, 2020b)
- Fushiki et al. (2016)
- Gerhard et al. (2017)
- Heckscher et al. (2015)
- Hueckesfeld et al. (2020)
- Imambocus et al.
- Jovanic et al. (2019)
- Jovanic, Schneider-Mizell et al. (2016)
- Larderet, Fritsch et al. (2017)
- Mark et al. (2019)
- Miroschnikow et al. (2018)
- Ohyama, Schneider-Mizell et al. (2015)
- Schlegel et al. (2016)
- Takagi et al. (2017)
- Tastekin et al. (2018)
- Valdes-Aleman et al. (2021)
- Winding, Pedigo et al. (2023)
- Zarin, Mark et al. (2019)
- Zwart et al. (2016)
Full references for specific neurons can be found on Virtual Fly Brain by searching for their skeleton ID (skid).
Dataset Contents
The viewer provides access to:
- Complete electron microscopy volume of a Drosophila first instar larva brain
- Manually traced neuron reconstructions from multiple research groups
- Synaptic connectivity information
- Associated metadata and annotations
Features
This CATMAID instance enables:
- Browser-based visualization of the serial section electron microscopy data
- Navigation through image stacks
- Viewing of neuron reconstructions
- Analysis of synaptic connectivity
- Data export functionality
Available Tools
- Tracing tool for examining reconstructions
- Neuron search interface with paper-based filtering
- Connectivity analysis tools
- Skeleton visualization options
- API access for programmatic data retrieval (documentation: https://catmaid.readthedocs.io/en/stable/api.html): https://l1em.catmaid.virtualflybrain.org/apis/
Citation Guidelines
When using this data, please cite:
-
The L1EM dataset: Winding M, et al. (2023) The connectome of an insect brain. Science, 379(6636):eadd9330. https://doi.org/10.1126/science.add9330
-
The CATMAID platform: Saalfeld S, Cardona A, Hartenstein V, Tomančák P (2009) CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25(15): 1984-1986. https://doi.org/10.1093/bioinformatics/btp266
-
The specific publication(s) associated with any neurons you analyze or reference (see Contributing Publications section)
Maintenance & Support
This resource is archived, hosted, and maintained by Virtual Fly Brain (VFB - https://virtualflybrain.org) as part of their commitment to preserving and making accessible critical Drosophila neuroscience data resources.