Publications

Publications

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.

2021

• Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein,Kun Song & Moritz Helmstaedter.
  Postnatal connectomic development of inhibition in mouse barrel cortex.
  Science (2021) DOI: 10.1126/science.abb4534.

• Yunfeng Hua, Xu Ding, Haoyu Wang, Fangfang Wang, Yan Lu, Jakob Neef, Yunge Gao, Tobias Moser & Hao Wu.
  Electron Microscopic Reconstruction of Neural Circuitry in the Cochlea.
  Cell Reports 34 (2021) DOI: 10.1101/2020.01.04.894816.

• Haoyu Wang, Shengxiong Wang, Yan Lu, Ying Chen, Wenqing Huang, Miaoxin Qiu, Hao Wu & Yunfeng Hua.
  Cytoarchitecture and innervation of the mouse cochlear amplifier revealed by large‐scale volume electron microscopy.
  J Comp Neurol. (2021) DOI: 10.1002/cne.25137.

• Carles Bosch, Tobias Ackels, Alexandra Pacureanu, Yuxin Zhang, Christopher J. Peddie, Manuel Berning, Norman Rzepka, Marie-Christine Zdora, Isabell Whiteley, Malte Storm, Anne Bonnin, Christoph Rau, Troy Margrie, Lucy Collinson & Andreas T. Schaefer.
  Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy.
  bioRxiv (2021) DOI: 10.1101/2021.01.13.426503.

2020

• Rafael Vescovi, Hanyu Li, Jeffery Kinnison, Murat Keceli, Misha Salim, Narayanan Kasthuri, Thomas D. Uram & Nicola Ferrier.
  Toward an Automated HPC Pipeline for Processing Large Scale ElectronMicroscopy Data.
  IEEE/ACM (2020) DOI: 10.1109/XLOOP51963.2020.00008.

• Ali Karimi.
  Connectomic analysis of apical dendrite innervation in pyramidal neurons of mouse cerebral cortex.
  Johann Wolfgang Goethe University (2020) urn:nbn:de:hebis:30:3-548308.

2019

• Alessandro Motta, Manuel Berning, Kevin M. Boergens, Benedikt Staffler, Marcel Beining, Sahil Loomba, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter. Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science (2019) DOI: 10.1126/science.aay3134.

• 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.

• Benedikt Sebastian Staffler.
  Machine Learning for Connectomics.
  Technical University Munich (2019) urn:nbn:de:bvb:91-diss-20190128-1449120-1-0.

• Ray L. Hong, Metta Riebesell, Daniel J. Bumbarger, Steven J. Cook, Heather R. Carstensen, Tahmineh Sarpolaki, Luisa Cochella, Jessica Castrejon, Eduardo Moreno, Bogdan Sieriebriennikov, Oliver Hobert & Ralf J. Sommer.
  Evolution of neuronal anatomy and circuitry in two highly divergent nematode species.
  eLife (2019) DOI: 10.7554/eLife.47155.001

2018

• 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.

• Kevin Boergens & Alexander Borst.
  Connectomic analysis of mouse barrel cortex and fly optic lobe.
  Ludwig Maximilians University (LMU) (2018) DOI: 10.5282/edoc.21829.

• Helene Schmidt-Helmstaedter.
  Large-scale circuit reconstruction in medial entorhinal cortex.
  Humboldt-Universität zu Berlin (2018) DOI: 10.18452/19197.

• Philip Alex Michael Laserstein. Connectomic analysis of the input to the principal cells of the mammalian cerebral
  cortex.
  Ludwig Maximilians University (LMU) (2018) DOI: 10.5282/edoc.21980.

• Eliot Dow, Adrian Jacobo, Sajjad Hossain, Kimberly Siletti & A. J. Hudspeth.
  Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit.
  eLife (2018) DOI: 10.7554/eLife.33988.001.

2017

• 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.

• Philipp Schlegel, Marta Costa & Gregory SXE Jefferis.
  Learning from connectomics on the fly.
  Current Opinion in Insect Science (2017) DOI: 10.17863/CAM.22119.

2015

• Manuel Berning, Kevin M.Boergens & Moritz Helmstaedter.
  SegEM: Efficient Image Analysis for High-Resolution Connectomics.
  Neuron Volume 87, Issue 6 (2015) DOI:10.1016/j.neuron.2015.09.003.