The EM image volume

Browse online - courtesy of the Virtual Fly Brain project
Download and trace locally - a preconfigured CATMAID installation
Download - losslessly compressed image tiles


This was a large, team effort executed over several years. Please see the author list and acknowledgements section of the paper (above) for contributors. Some coverage + press:
Cell video abstract
In a ‘tour de force,’ researchers image an entire fly brain in minute detail - Science magazine
Complete Fly Brain Imaged at Nanoscale Resolution - HHMI News
Every Neuron of a Fruit Fly Brain, In Nanoscopic Detail - Discover
This colorful web is the most complete look yet at a fruit fly’s brain cells - ScienceNews
Explore This Exquisitely Detailed 3D Brain - National Geographic
3D image reveals hidden neurons in fruit-fly brain - Nature
Finalist in 2018 Breakthrough of the year - Science

The tracing community

As of July 2018, this community has two components: (1), a group tracing in a collaborative 'walled garden' in a CATMAID server hosted by the Bock lab, in 'open lab notebook' fashion; and (2), independent tracers who have downloaded the dataset and are running their own CATMAID (or whatever) servers. Laboratories participating in (1) include:
  • Davi Bock - Janelia Research Campus
  • Gwyneth Card - Janelia Research Campus
  • Eugenia Chiappe - Champalimaud
  • Barry Dickson - Janelia Research Campus
  • Andrew Dacks - West Virginia University
  • Stephen Huston - Janelia Research Campus
  • Vivek Jayaraman - Janelia Research Campus
  • Greg Jefferis - MRC LMB; University of Cambridge
  • Ilona Grunwald Kadow - Technical University of Munich
  • Azusa Kamikouchi - Nagoya University
  • Matthias Landgraf - University of Cambridge
  • Thomas Preat - ESPCI-CNRS
  • Michael Reiser - Janelia Research Campus
  • Gerry Rubin - Janelia Research Campus
  • Kristin Scott - UC Berkeley
  • Andrew Seeds & Steffi Hampel - University of Puerto Rico
  • Gaia Tavosanis - German Center for Neurodegenerative Diseases DZNE
  • Scott Waddell - Oxford University
  • Mathias Wernet - Freie Universitat Berlin
  • Rachel Wilson - Harvard University
  • How to join

    The 'walled garden' community is managed by Marta Costa, with Davi Bock, Greg Jefferis and Michael Reiser also on the management board. If you are interested in joining, please contact Marta Costa.

    Tools for data analysis

  • NeuroAnatomy Toolbox (nat): R package for toolset for analysing neuron structure/circuit organisation
  • rcatmaid: R package to interact with CATMAID
  • elmr: R package that builds on the elm package, to bridge EM and light datasets, including neuronal similarity comparisons
  • Electron-Light Microscopy (elm): defines a transformation between light level data and EM
  • CATMAID Blender plugin: allows Blender to interact with CATMAID to generate 3D movies or meshes
  • CATMAID Python package (Pymaid): python package to interact with CATMAID
  • Tools and scripts listing (R and python): links to useful tools and bespoke scripts used by the FAFB community