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://flyconnecto.me/
• 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:

• Circuit reorganization in the Drosophila mushroom body calyx accompanies memory consolidation (Baltruschat et al. 2021)
• Complete connectome of the Drosophila mushroom body provides insights into memory organization (Bates and Schlegel et al. 2020)
• The Connectome of the Adult Drosophila Mushroom Body Provides Insights into Function (Coates et al. 2020)
• Integration of the olfactory code across dendritic claws of single mushroom body neurons (Dolan and Belliart-Guérin et al. 2018)
• Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body (Dolan et al. 2019)
• Drosophila gustatory projections are segregated by taste modality and connectivity (Engert et al. 2022)
• Re-evaluation of learned information in Drosophila (Felsenberg et al. 2018)
• Motor neurons generate pose-targeted movements via proprioceptive sculpting (Gorko et al. 2024)
• Distinct subpopulations of mechanosensory chordotonal organ neurons elicit grooming of the fruit fly antennae (Hampel et al. 2020)
• A neural circuit for wind-guided olfactory navigation (Kim et al. 2020)
• Parallel encoding of sensory history and behavioral preference during Caenorhabditis elegans olfactory learning (Kind et al. 2021)
• A neural circuit for diurnal temperature preference in Drosophila (Marin et al. 2020)
• Spatial readout of visual looming in the central brain of Drosophila (Morimoto et al. 2020)
• Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila (Otto et al. 2020)
• A Neural Circuit Architecture for Angular Integration in Drosophila (Sayin et al. 2019)
• Taste quality and hunger interactions in a feeding sensorimotor circuit (Shiu et al. 2022)
• Generating parallel representations of position and identity in the olfactory system (Taisz et al. 2023)
• A synaptic threshold mechanism for computing escape decisions (Turner-Evans et al. 2020)
• Neural circuitry linking mating and egg laying in Drosophila females (Wang et al. 2020a)
• Circuit and Behavioral Mechanisms of Sexual Rejection by Drosophila Females (Wang et al. 2020b)
• Neural circuit mechanisms of sexual receptivity in Drosophila females (Wang et al. 2020c)
• Zhao et al. (2023)
• Structured sampling of olfactory input by the fly mushroom body (Zheng et al. 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/

Public API token

Read-only access to this instance is open to everyone, but most of CATMAID’s query endpoints are POST rather than GET, and POST requests are subject to a CSRF check. Command-line and server-side clients (pymaid, curl, scripts) can satisfy that check by requesting a page first and replaying the cookie they are given. Code running in a browser cannot: it can neither read a cookie belonging to another site nor set a Referer header. Browser-based tools should therefore authenticate as the anonymous user, using this token:

3ca85fe2f8351ae8f4550f050ab8c0815d53f576

This token is published deliberately and is not a secret. It authenticates as AnonymousUser, whose only permission on this project is can_browse, so it grants exactly the read access this page already offers to everyone and nothing further. Write requests made with it are refused by the server.

Send it in either the X-Authorization or the Authorization header:

curl -X POST https://fafb.catmaid.virtualflybrain.org/1/skeleton/neuronnames \
  -H "X-Authorization: Token 3ca85fe2f8351ae8f4550f050ab8c0815d53f576" \
  --data "skids[0]=16"

Citation Guidelines

When using this data, please cite:

1. 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

2. 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

3. 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.