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

About

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:
  • Erin Barnhart - Columbia University
  • Davi Bock - University of Vermont/Janelia Research Campus
  • Gwyneth Card - Janelia Research Campus
  • Eugenia Chiappe - Champalimaud
  • Barry Dickson - Janelia Research Campus
  • Andrew Dacks - West Virginia University
  • Sarah Farris - West Virginia University
  • Mark Frye - UCLA
  • Volker Hartenstein - University of California, Los Angeles
  • Bassem Hassam - Sorbonne University, Paris
  • 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
  • Wei-Chung Lee - Harvard University
  • Marion Silies - Johannes-Gutenberg-Universität Mainz
  • Thomas Preat & Pierre-Yves Plaçais - ESPCI-CNRS
  • Ronny Rosner - Newcastle University
  • 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, Bonn
  • 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 steering committee. If you are interested in joining, please contact Marta Costa.

    FAFB Publications

  • Kim et al. (2020) Wiring patterns from auditory sensory neurons to the escape and song‐relay pathways in fruit flies, The Journal of Comparative Neurology
  • Sayin et al. (2019) A neural circuit arbitrates between perseverance and withdrawal in hungry Drosophila, Neuron
  • Dolan et al. (2019) Neurogenetic dissection of the Drosophila lateral horn reveals output, functions and interaction with the mushroom body. eLife
  • Frechter et al. (2019) Functional and anatomical specificity in a higher olfactory centre. eLife
  • Dolan, Belliart-Guérin et al. (2018) Communication from Learned to Innate Olfactory Processing Centers Is Required for Memory Retrieval in Drosophila. Neuron
  • Felsenberg et al. (2018) Integration of Parallel Opposing Memories Underlies Memory Extinction. Cell

  • Preprints

  • Marin et al. (2020) Connectomics analysis reveals first, second, and third order thermosensory and hygrosensory neurons in the adult Drosophila brain, bioRxiv
  • Turner-Evans et al. (2020) The neuroanatomical ultrastructure and function of a biological ring attractor, bioRxiv
  • Bates and Schlegel et al. (2020) Complete connectomic reconstruction of olfactory projection neurons in the fly brain, bioRxiv
  • Li et al. (2019) Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment, bioRxiv
  • Zhang et al. (2019) Regulation of modulatory cell activity across olfactory structures in Drosophila melanogaster, bioRxiv
  • Dolan et al. (2018) Neurogenetic dissection of the Drosophila innate olfactory processing center, bioRxiv
  • Huoviala et al. (2018) Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending outputbioRxiv
  • Frechter et al. (2018) Functional and Anatomical Specificity in a Higher Olfactory CentrebioRxiv
  • Sayin et al. (2018) A neural circuit arbitrates between perseverance and withdrawal in hungry Drosophila, bioRxiv
  • Dolan, Belliart-Guerin et al. (2017) Communication from learned to innate olfactory processing centres is required for memory retrieval in DrosophilabioRxiv
  • Zheng, Lauritzen et al. (2017) A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogasterbioRxiv

  • Papers citing Zheng, Lauritzen et al. 2018 Cell

    Tools for data analysis

  • The natverse: A collection of interoperable R packages to import, visualise, analyse, manipulate and export 3D neuroanatomical data. The most relevant ones for EM data are mentioned below.
  • 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