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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.


  • 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


  • 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