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:

1. 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

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.