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L1EM CATMAID Data Viewer

This CATMAID (Collaborative Annotation Toolkit for Massive Amounts of Image Data) instance hosts neuroanatomical data from the Drosophila first instar larva (L1) electron microscopy dataset, featuring manually traced neurons from numerous research publications.

Drosopila Larval CNS 70% traced back in 2017

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

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

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:

4c1c9c60d4864c41ebc79f42ba99014a9e912f49

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://l1em.catmaid.virtualflybrain.org/1/skeleton/neuronnames \
  -H "X-Authorization: Token 4c1c9c60d4864c41ebc79f42ba99014a9e912f49" \
  --data "skids[0]=16"

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.