TY - JOUR TI - FluoEM, virtual labeling of axons in three-dimensional electron microscopy data for long-range connectomics AU - Drawitsch, Florian AU - Karimi, Ali AU - Boergens, Kevin M AU - Helmstaedter, Moritz A2 - Nathans, Jeremy A2 - Marder, Eve VL - 7 PY - 2018 DA - 2018/08/14 SP - e38976 C1 - eLife 2018;7:e38976 DO - 10.7554/eLife.38976 UR - https://doi.org/10.7554/eLife.38976 AB - The labeling and identification of long-range axonal inputs from multiple sources within densely reconstructed electron microscopy (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. KW - connectomics KW - electron microscopy KW - light microscopy KW - cerebral cortex JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -