FluoEM, virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics
- Max Planck Institute for Brain Research, Germany
Abstract
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.
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FluoEM low-res EM datasetFluoEM_2016-05-23_FD0144-2_st001_v1, openly accessible via webknossos.org.
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FluoEM high-res EM datasetFluoEM_2016-05-26_FD0144-2_v2s2s, openly accessible via webknossos.org.
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FluoEM LM datasetFluoEM_2016-06-02-FD0144_2_Confocal , openly accessible via webknossos.org.
Article and author information
Author details
Moritz Helmstaedter
Funding
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.
Reviewing Editor
- Jeremy Nathans, Johns Hopkins University School of Medicine, United States
Ethics
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.
Version history
- Received: June 6, 2018
- Accepted: August 10, 2018
- Accepted Manuscript published: August 14, 2018 (version 1)
- Version of Record published: September 21, 2018 (version 2)
Copyright
© 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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FluoEM, virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics
eLife 7:e38976.
https://doi.org/10.7554/eLife.38976
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