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

Abstract
Data availability
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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.

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.

https://demo.webknossos.org/datasets/FluoEM_2016-05-23_FD0144-2_st001_v1/view
1. Drawitsch F
2. Helmstaedter M
(2018) FluoEM high-res EM dataset
FluoEM_2016-05-26_FD0144-2_v2s2s, openly accessible via webknossos.org.

https://demo.webknossos.org/datasets/FluoEM_2016-05-26_FD0144-2_v2s2s/view
1. Drawitsch F
2. Helmstaedter M
(2018) FluoEM LM dataset
FluoEM_2016-06-02-FD0144_2_Confocal , openly accessible via webknossos.org.

https://demo.webknossos.org/datasets/FluoEM_2016-06-02-FD0144_2_Confocal/view

Article and author information

Author details

Florian Drawitsch

Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany

Competing interests
No competing interests declared.
Ali Karimi

Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany

Competing interests
No competing interests declared.
Kevin M Boergens

Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany

Competing interests
No competing interests declared.
Moritz Helmstaedter

Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany

For correspondence
mh@brain.mpg.de

Competing interests
Moritz Helmstaedter, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0001-7973-0767

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.

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.

Copyright

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.