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.

2023

• Tri M. Nguyen, Logan A. Thomas, Jeff L. Rhoades, Ilaria Ricchi, Xintong Cindy Yuan, Arlo Sheridan, David G. C. Hildebrand, Jan Funke, Wade G. Regehr & Wei-Chung Allen Lee.
  Structured cerebellar connectivity supports resilient pattern separation.
  Nature (2023). DOI: 10.1038/s41586-022-05471-w

• Wan Qing Yu, Rachael Swanstrom, Crystal L. Sigulinsky, Richard M. Ahlquist, Sharm Knecht, Bryan W. Jones, David M. Berson & Rachel O. Wong.
  Distinctive synaptic structural motifs link excitatory retinal interneurons to diverse postsynaptic partner types.
  Cell Reports (2023). DOI: 10.1016/j.celrep.2023.112006

• Kun Song, Zhihui Feng & Moritz Helmstaedter.
  High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics.
  Nature Methods (2023). DOI: 10.1101/2022.03.30.486341

• Tri Nguyen, Mukul Narwani, Mark Larson, Yicong Li, Shuhan Xie, Hanspeter Pfister, Donglai Wei, Nir Shavit, Lu Mi, Alexandra Pacureanu, Wei-Chung Lee & Aaron T. Kuan.
  The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletons.
  arXiv (2023). DOI: 10.48550/arXiv.2302.03819

2022

• Sahil Loomba, Jakob Straehle, Vijayan Gangadharan, Natalie Heike, Abdelrahman Khalifa, Alessandro Motta, Niansheng Ju, Meike Sievers, Jens Gempt, Hanno S. Meyer & Moritz Helmstaedter.
  Connectomic comparison of mouse and human cortex.
  Science (2022). DOI: 10.1126/science.abo0924.
  View data in WEBKNOSSOS.

• 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.
  Nature Communications (2022) DOI: 10.1038/s41467-022-30199-6.

• Vijayan Gangadharan, Hongwei Zheng, Francisco J. Taberner, Jonathan Landry, Timo A. Nees, Jelena Pistolic, Nitin Agarwal, Deepitha Männich, Vladimir Benes, Moritz Helmstaedter, Björn Ommer, Stefan G. Lechner, Thomas Kuner & Rohini Kuner.
  Neuropathic pain caused by miswiring and abnormal end organ targeting.
  Nature (2022). DOI: 10.1038/s41586-022-04777-z.
  View data in WEBKNOSSOS.

• Jialei Zhou, Haibin Sheng, Haoyu Wang, Yan Lu, Fangfang Wang, Hao Wu, Yunfeng Hua.
  Application of three-dimensional electron microscopy to morphological study of neurons in brainstem cochlear nucleus.
  Journal of Shanghai Jiaotong university (Medical Science) (2022). DOI: 10.3969/j.issn.1674-8115.2022.02.002

• Yuxin Zhang, Tobias Ackels, Alexandra Pacureanu, Marie-Christine Zdora, Anne Bonnin, Andreas T. Schaefer, Carles Bosch.
  Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy.
  Frontiers in Cell and Development al Biology (2022). DOI: 10.3389/fcell.2022.880696

• Daniela Chequer Charan, Yunfeng Hua, Haoyu Wang, Wenqing Huang, Fangfang Wang, Ana Belén Elgoyhen, Kevin M Boergens & Mariano N Di Guilmi. Volume electron microscopy reveals age-related circuit remodeling in the auditory brainstem.
  Frontiers in Cellular Neuroscience (2022). DOI: 10.3389/fncel.2022.1070438

• Yong Fan, Chenhui Huang, Juan Chen, Yanyan Chen, Yan Wang, Zhiguang Yan , Weina Yu, Haibo Wu, Ying Yang, Leit ong Nie, Sijia Huang, Fangfang Wang, H aoyu Wang, Yunfeng Hua, Qifeng Lyu, Yanping Kuang & Ming Lei.
  Mutations in CCIN cause teratozoospermia and male infertility.
  Science Bulletin (2022). DOI: 10.1016/j.scib.2022.09.026

• Anthony Santella, Irina Kolotuev, Caroline Kizilyaprak & Zhirong Bao.
  Cross-modality synthesis of EM time series and live fluorescence imaging.
  Elife (2022). DOI: 10.7554/eLife.77918
  View data in WEBKNOSSOS

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.
  View data in WEBKNOSSOS.

• 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.
  View data in WEBKNOSSOS.

• 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.

• Vandana Sampathkumar, Andrew Miller-Hansen, S. Murray Sherman, Narayanan Kasthuri.
  Integration of signals from different cortical areas in higher order thalamic neurons.
  Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2104137118

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.

• Vandana Sampathkumar, Andrew Miller-Hansen, S. Murray Sherman, Narayanan Kasthuri.
  An ultrastructural connectomic analysis of a higher-order thalamocortical circuit in the mouse.
  European Journal of Neuroscience (2020). DOI: 10.1111/ejn.15092

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.
  View data in WEBKNOSSOS.

• 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.
  View data in WEBKNOSSOS.

• 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.
  View data in WEBKNOSSOS.

• 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.
  View data in WEBKNOSSOS.

• 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.
  View data in WEBKNOSSOS.

2017

• Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler & 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.
  View data in WEBKNOSSOS.

• 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.