The following publications used webKnossos for exploring large 3D electron-microscopy (EM) and light-microscopy (LM) datasets as well as collaboratively generating annotations or other tasks. Please get in touch with us if your publication is missing.


  • Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter.

    Cell-type specific innervation of cortical pyramidal cells at their apical tufts.

    bioRxiv (2019) DOI:10.1101/571695.


  • Kevin M. Boergens, Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst. Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset. PLOS ONE (2018) DOI:10.1371/journal.pone.0207828.

  • Florian Drawitsch, Ali Karimi, Kevin M Boergens, Moritz Helmstaedter. FluoEM, virtual labeling of axons in threedimensional electron microscopy data for long-range connectomics. eLife (2018) DOI:10.7554/eLife.38976.001.

  • Alessandro Motta, Manuel Berning, Kevin M. Boergens, Benedikt Staffler, Marcel Beining, Sahil Loomba, Christian Schramm, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter. Dense connectomic reconstruction in layer 4 of the somatosensory cortex. bioRxiv (2018) DOI:10.1101/460618.


  • Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter. webKnossos: efficient online 3D data annotation for connectomics. Nature Methods (2017) DOI:10.1038/NMETH.4331.

  • Helene Schmidt, Anjali Gour, Jakob Straehle, Kevin M. Boergens, Michael Brecht & Moritz Helmstaedter. Axonal synapse sorting in medial entorhinal cortex. Nature (2017) DOI:10.1038/nature24005.

  • Benedikt Staffler, Manuel Berning, Kevin M Boergens, Anjali Gour, Patrick van der Smagt & Moritz Helmstaedter. SynEM, automated synapse detection for connectomics. eLife (2017) DOI:10.7554/eLife.26414.