1. Neuroscience
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FluoEM, virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics

  1. Florian Drawitsch
  2. Ali Karimi
  3. Kevin M Boergens
  4. Moritz Helmstaedter  Is a corresponding author
  1. Max Planck Institute for Brain Research, Germany
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Cite this article as: eLife 2018;7:e38976 doi: 10.7554/eLife.38976


The labeling and identification of long-range axonal inputs from multiple sources within densely reconstructed EM datasets from mammalian brains has been notoriously difficult because of the limited color label space of EM. Here, we report FluoEM for the identification of multi-color fluorescently labeled axons in dense EM data without the need for artificial fiducial marks or chemical label conversion. The approach is based on correlated tissue imaging and computational matching of neurite reconstructions, amounting to a virtual color labeling of axons in dense EM circuit data. We show that the identification of fluorescent light- microscopically (LM) imaged axons in 3D EM data from mouse cortex is faithfully possible as soon as the EM dataset is about 40-50 µm in extent, relying on the unique trajectories of axons in dense mammalian neuropil. The method is exemplified for the identification of long-distance axonal input into layer 1 of the mouse cerebral cortex.

Data availability

All imaging data is available for online browsing and annotation at demo.webknossos.org as detailed in the data availability section of the Methods.

The following data sets were generated
    1. Drawitsch F
    2. Helmstaedter M
    (2018) FluoEM low-res EM dataset
    FluoEM_2016-05-23_FD0144-2_st001_v1, openly accessible via webknossos.org.
    1. Drawitsch F
    2. Helmstaedter M
    (2018) FluoEM high-res EM dataset
    FluoEM_2016-05-26_FD0144-2_v2s2s, openly accessible via webknossos.org.
    1. Drawitsch F
    2. Helmstaedter M
    (2018) FluoEM LM dataset
    FluoEM_2016-06-02-FD0144_2_Confocal , openly accessible via webknossos.org.

Article and author information

Author details

  1. Florian Drawitsch

    Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  2. Ali Karimi

    Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  3. Kevin M Boergens

    Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  4. Moritz Helmstaedter

    Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
    For correspondence
    Competing interests
    Moritz Helmstaedter, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7973-0767


Max-Planck-Gesellschaft (Open-access funding)

  • Florian Drawitsch
  • Ali Karimi
  • Kevin M Boergens
  • Moritz Helmstaedter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.


Animal experimentation: All experimental procedures were performed according to the law of animal experimentation issued by the German Federal Government under the supervision of local ethics committees and according to the guidelines of the Max Planck Society. The experimental procedures were approved by Regierungspräsidium Darmstadt, V54 - 19c20/15 - F126/1015.

Reviewing Editor

  1. Jeremy Nathans, Johns Hopkins University School of Medicine, United States

Publication history

  1. Received: June 6, 2018
  2. Accepted: August 10, 2018
  3. Accepted Manuscript published: August 14, 2018 (version 1)
  4. Version of Record published: September 21, 2018 (version 2)


© 2018, Drawitsch et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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