The fruit fly Drosophila melanogaster currently has the best mapped nervous system of any animal. This is because the fly nervous system has now been extensively charted in connectomes – wiring diagrams that trace the anatomy and connectivity of all the cells in the brain and nerve cord (the equivalent of the mammalian spinal cord).
The rapid evolution of Drosophila connectomics has given rise to a diverse ecosystem of open-access resources, which now includes six different datasets that vary in image acquisition, resolution, proofreading status, annotation density, covered region, and sex of the animals. These resources live on different platforms and have their own custom toolkits for data analysis.
While connectomes offer a wealth of information, actually accessing and processing these data can be confusing.
This post is a practical guide to the existing adult Drosophila connectomes, focusing on:
- the contents of each dataset,
- how to access them, and
- how to cite them.
Why flies?
Until recently, mapping neural circuits at scale was limited to the resolution of available molecular tracing methods, including anterograde and retrograde viral systems (Callaway and Luo 2015; Zingg et al. 2017; Lo and Anderson 2011), molecular proximity labelling (Feinberg et al. 2008; Y. Li et al. 2016), and synthetic signalling pathways (Barnea et al. 2008; Jagadish et al. 2014; Talay et al. 2017). Now, electron microscopy (EM) achieves sufficient resolution to create synaptic-resolution wiring diagrams, or connectomes. This technique offers a highly specific method for investigating the anatomy and connectivity of cells in the nervous system, complete with sharp structural contrast for dense reconstruction of cells, synaptic structures, and intracellular components. The catch is that EM volume connectomes can be expensive and time-consuming to produce.
Although improvements have been made to increase the cost-benefit ratio of EM datasets, further technological advances are required to scale this technique from the current technical limit, 1 cubic millimetre, to the size of a full mouse brain, around 500 cubic millimetres. Given these limitations, the adult fruit fly nervous system is the current frontier of whole-brain EM connectomics. The relatively simple nervous system of Drosophila melanogaster, in combination with large amounts of light microscopy-based image data and advanced molecular genetic tools, have made it an ideal model system for constructing circuit maps.
Adult Drosophila connectomes
Several adult Drosophila connectome datasets currently exist. The available adult Drosophila EM connectomes are summarised in Table 1. Here, we walk through available tooling, data repositories, and how to get programmatic access to different datasets.
Table 1: Adult Drosophila connectomes
| Dataset | hemibrain | FAFB/FlyWire | FANC | MANC | MaleCNS | BANC |
| Sex | Female | Female | Female | Male | Male | Female |
| Region | 1/3 brain | whole brain | VNC | VNC | whole CNS | whole CNS |
| Acquisition | FIB-SEM | ssTEM | ssTEM | FIB-SEM | FIB-SEM | ssTEM |
| Resolution | 8x8x8 nm | 4×4×40 nm | 4.3×4.3×4.3nm | 8x8x8 nm | 8x8x8 nm | 4x4x45 nm |
| Data type | dense | dense | sparse | dense | dense | sparse |
| # neurons | 25k | 140k | 14.6k | 15.8k | 167k | 142k |
| Repository | neuPrint | Codex | GitHub | neuPrint | neuPrint | Codex |
| Publication | Scheffer et al., 2020 | Zheng et al., 2018 (FAFB EM volume) Dorkenwald et al., 2024 (FlyWire segmentation) Schlegel et al., 2024 (Annotations) | Phelps et al.2021 (dataset) Azevedo et al., 2024(reconstruction) | Takemura et al., 2024 (dataset) Marin et al., 2024 (annotations) | Berg etal., 2026 | Bates et al., 2026 |
Brains
For the last half of the decade, Drosophila brain connectomes have enabled large-scale investigations into neural processing. For example, sensory systems, like the olfactory antennal lobe (AL) (Alexander S. Bates et al. 2020; Schlegel et al. 2021) and optic lobes (OL) (Nern et al. 2025), and entire brain regions including the mushroom body (MB) (F. Li et al. 2020) and central complex (CX) (Hulse et al. 2021), have been completely reconstructed and extensively analyzed. Recent studies have also used the FAFB/FlyWire dataset to predict behaviour (Sapkal et al. 2024), and to model sensorimotor processing (Shiu et al. 2024).
Hemibrain
The hemibrain dataset was the first large-scale dense reconstruction of a Drosophila brain, covering roughly one third of the central brain (~25,000 neurons).
How to access: neuPrint hemibrainv:1.2.1
Visualization: Neuroglancer
Analysis tools: hemibrainr (R)
How to cite: Scheffer et al., 2020
FAFB/FlyWire
The FAFB (full adult fly brain) volume and its FlyWire segmentation represent the first complete whole brain connectome, containing 140,000 neurons.
How to access: Codex
Visualization: FlyWire
Analysis tools: fafbseg (R)
How to cite: Zheng et al., 2018 (FAFB EM volume)
Dorkenwald et al., 2024 (FlyWire segmentation)
Schlegel et al., 2024 (Annotations)
Further guidelines for citing FAFB/FlyWire data can be found here.
Nerve cords
Two connectome volumes of a female adult ventral nerve cord (FANC) and a male adult ventral nerve cord (MANC) complement the brain volumes, enabling investigation of sensory and motor circuits in the legs and abdomen as well as ascending and descending neurons that traverse the neck (Marin et al. 2024; Lesser et al. 2024; Cheong et al. 2025; Stürner et al. 2025; Azevedo et al. 2024; Phelps et al. 2021).
FANC
How to access: GitHub FANC_auto_recon
Visualization: Neuroglancer
Analysis tools: fancr (R)
How to cite: Phelps et al., 2021 (dataset)
Azevedo et al., 2024 (reconstruction)
MANC
How to access: neuPrint MANCv:1.2.3
Visualization: Neuroglancer
Analysis tools: malevnc (R)
How to cite: Takemura et al., 2024 (dataset)
Marin et al., 2024 (annotations)
Whole CNS
The latest datasets in the Drosophila connectome ecosystem unite the brain and nerve cord into a single continuous connectome through an intact neck connective. These datasets now enable full sensory-to-motor tracing of circuits across the entire nervous system.
Male CNS
The male CNS connectome, a whole CNS that includes the first male fly brain connectome, consists of 166,700 neurons spanning the central brain, optic lobes, and ventral nerve cord. This dataset is the largest and most complete Drosophila connectome to date, with 99% of nuclei associated with a proofread neuron, and over 13,000 unique annotations.
How to access: neuPrint malecns:v1.0
Visualization: Neuroglancer
Analysis tools: malecns (R)
How to cite: Berg et al., 2026
BANC
The Brain And Nerve Cord (BANC) connectome contains the complete female central nervous system, uniting the brain and nerve cord through an intact neck. This dataset includes highly detailed annotations of the neurons innervating sensory organs, motor neurons, and viscera throughout the fly body.
Analysis tools: bancr (R)
How to cite: Bates et al., 2026
Getting started
Getting access to connectome data is the first step in the analysis pipeline. For the neuPrint datasets, you’ll need to supply a neuPrint token, which is easily attainable by signing up for an account on the neuPrint website. CAVE-based data requires setting up a client, the instructions for which can be found here.
The existing tooling for analysis differs according to programming language. Most of the tools were built in R and Python, and are included as part of the natverse (Alexander Shakeel Bates et al. 2020) and navis suites. These include tutorials and examples for installing and using the packages.
References
Azevedo, Anthony, Ellen Lesser, Jasper S. Phelps, et al. 2024. “Connectomic Reconstruction of a Female Drosophila Ventral Nerve Cord.” Nature 631 (8020): 360–368.
Barnea, Gilad, Walter Strapps, Gilles Herrada, et al. 2008. “The Genetic Design of Signaling Cascades to Record Receptor Activation.” Proceedings of the National Academy of Sciences of the United States of America 105 (1): 64–69.
Bates, Alexander Shakeel, James D. Manton, Sridhar R. Jagannathan, et al. 2020. The Natverse, a Versatile Toolbox for Combining and Analysing Neuroanatomical Data. April 14. https://doi.org/10.7554/eLife.53350.
Bates, Alexander S., Philipp Schlegel, Ruairi J. V. Roberts, et al. 2020. “Complete Connectomic Reconstruction of Olfactory Projection Neurons in the Fly Brain.” Current Biology : CB 30 (16): 3183–3199.e6.
Callaway, Edward M., and Liqun Luo. 2015. “Monosynaptic Circuit Tracing with Glycoprotein-Deleted Rabies Viruses.” The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 35 (24): 8979–8985.
Cheong, Han S. J., Katharina Eichler, Tomke Stürner, et al. 2025. “Transforming Descending Input into Motor Output: An Analysis of the Drosophila Male Adult Nerve Cord Connectome.” July 21. https://doi.org/10.7554/elife.96084.2.
Feinberg, Evan H., Miri K. Vanhoven, Andres Bendesky, et al. 2008. “GFP Reconstitution Across Synaptic Partners (GRASP) Defines Cell Contacts and Synapses in Living Nervous Systems.” Neuron 57 (3): 353–363.
Hulse, Brad K., Hannah Haberkern, Romain Franconville, et al. 2021. “A Connectome of the Drosophila Central Complex Reveals Network Motifs Suitable for Flexible Navigation and Context-Dependent Action Selection.” eLife 10 (October). https://doi.org/10.7554/eLife.66039.
Jagadish, Smitha, Gilad Barnea, Thomas R. Clandinin, and Richard Axel. 2014. “Identifying Functional Connections of the Inner Photoreceptors in Drosophila Using Tango-Trace.” Neuron 83 (3): 630–644.
Lesser, Ellen, Anthony W. Azevedo, Jasper S. Phelps, et al. 2024. “Synaptic Architecture of Leg and Wing Premotor Control Networks in Drosophila.” Nature 631 (8020): 369–377.
Li, Feng, Jack W. Lindsey, Elizabeth C. Marin, et al. 2020. “The Connectome of the Adult Drosophila Mushroom Body Provides Insights into Function.” eLife 9 (December). https://doi.org/10.7554/eLife.62576.
Li, Yiming, Aike Guo, and Hao Li. 2016. “CRASP: CFP Reconstitution across Synaptic Partners.” Biochemical and Biophysical Research Communications 469 (3): 352–356.
Lo, Liching, and David J. Anderson. 2011. “A Cre-Dependent, Anterograde Transsynaptic Viral Tracer for Mapping Output Pathways of Genetically Marked Neurons.” Neuron 72 (6): 938–950.
Marin, Elizabeth C., Billy J. Morris, Tomke Stürner, et al. 2024. “Systematic Annotation of a Complete Adult Male Drosophila Nerve Cord Connectome Reveals Principles of Functional Organisation.” July 22. https://doi.org/10.7554/elife.97766.1.
Nern, Aljoscha, Frank Loesche, Shin-Ya Takemura, et al. 2025. “Connectome-Driven Neural Inventory of a Complete Visual System.” Nature 641 (8065): 1225–1237.
Phelps, Jasper S., David Grant Colburn Hildebrand, Brett J. Graham, et al. 2021. “Reconstruction of Motor Control Circuits in Adult Drosophila Using Automated Transmission Electron Microscopy.” Cell 184 (3): 759–774.e18.
Sapkal, Neha, Nino Mancini, Divya Sthanu Kumar, et al. 2024. “Neural Circuit Mechanisms Underlying Context-Specific Halting in Drosophila.” Nature 634 (8032): 191–200.
Schlegel, Philipp, Alexander Shakeel Bates, Tomke Stürner, et al. 2021. “Information Flow, Cell Types and Stereotypy in a Full Olfactory Connectome.” eLife 10 (May). https://doi.org/10.7554/eLife.66018.
Shiu, Philip K., Gabriella R. Sterne, Nico Spiller, et al. 2024. “A Drosophila Computational Brain Model Reveals Sensorimotor Processing.” Nature 634 (8032): 210–219.
Stürner, Tomke, Paul Brooks, Laia Serratosa Capdevila, et al. 2025. “Comparative Connectomics of Drosophila Descending and Ascending Neurons.” Nature 643 (8070): 158–172.
Talay, Mustafa, Ethan B. Richman, Nathaniel J. Snell, et al. 2017. “Transsynaptic Mapping of Second-Order Taste Neurons in Flies by Trans-Tango.” Neuron 96 (4): 783–795.e4.
Zingg, Brian, Xiao-Lin Chou, Zheng-Gang Zhang, et al. 2017. “AAV-Mediated Anterograde Transsynaptic Tagging: Mapping Corticocollicular Input-Defined Neural Pathways for Defense Behaviors.” Neuron 93 (1): 33–47.