publications.md

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.

2025

• Jakob Reichmann, Anne Schnurpfeil, Sylvia Mittelstädt, Patrick Moller Jensen, Vedrana Andersen Dahl, Anders Bjorholm Dahl, Carina Weide, Eva von Campenhausen, Hector Dejea, Paul Tafforeau, Christopher Werlein, Danny Jonigk, Maximilian Ackermann, Klaus Engel, Julia Gallwas, Alexander Dietz, Mir Fuad Hasanov & Tim Salditt.
  3D multiscale characterization of the human placenta: Bridging anatomy and histology by X-ray phase-contrast tomography.
  PNAS Nexus, Volume 4, Issue 1 (2025). DOI: 10.1093/pnasnexus/pgae583

2024

• Andrea Nathansen, Matthis Clausen, Manuel Berning, Ethan MacKenzie, Yuxin Zhang, Alexandra Pacureanu, Andreas T. Schaefer, Norman Rzepka, & Carles Bosch.
  Cell nuclei segmentation in mm-scale x-ray holographic nanotomography images of mouse brain tissue.
  Developments in X-Ray Tomography XV. Vol. 13152. SPIE (2024). DOI: 10.1117/12.3028309
  View data #1 #2 in WEBKNOSSOS

• Anja Günther, Silke Haverkamp, Stephan Irsen, Paul V. Watkins, Karin Dedek, Henrik Mouritsen & Kevin L. Briggman.
  Species–specific circuitry of double cone photoreceptors in two avian retinas.
  Communications Biology 7.1 (2024). DOI: 10.1038/s42003-024-06697-2
  View data in WEBKNOSSOS

• Yan Lu, Jing Liu, Bei Li, Haoyu Wang , Fangfang Wang , Shengxiong Wang , Hao Wu , Hua Han & Yunfeng Hua.
  Spatial patterns of noise-induced inner hair cell ribbon loss in the mouse mid-cochlea.
  Iscience 27.2 (2024). DOI: 10.1016/j.isci.2024.108825
  View data #1 #2 #3 #4 #5 #6 in WEBKNOSSOS

• Meike Sievers, Alessandro Motta, Martin Schmidt, Yagmur Yener, Sahil Loomba, Kun Song, Johannes Bruett, & Moritz Helmstaedter.
  Connectomic reconstruction of a cortical column.
  bioRxiv (2024). DOI: 2024.03.22.586254

• Martin Schmidt, Alessandro Motta, Meike Sievers & Moritz Helmstaedter.
  RoboEM: automated 3D flight tracing for synaptic-resolution connectomics.
  Nature Methods 21.5 (2024). DOI: 10.1038/s41592-024-02226-5

• Rosanna P. Sammons, Mourat Vezir, Laura Moreno-Velasquez, Gaspar Cano, Marta Orlando, Meike Sievers, Eleonora Grasso, Verjinia D. Metodieva, Richard Kempter, Helene Schmidt, & Dietmar Schmitz.
  Structure and function of the hippocampal CA3 module.
  Proceedings of the National Academy of Sciences 121.6 (2024). DOI: 10.1073/pnas.2312281120

• Julia M. Michalska, Julia Lyudchik, Philipp Velicky, Hana Štefaničková, Jake F. Watson, Alban Cenameri, Christoph Sommer, Nicole Amberg, Alessandro Venturino, Karl Roessler, Thomas Czech, Romana Höftberger, Sandra Siegert, Gaia Novarino, Peter Jonas & Johann G. Danzl.
  Imaging brain tissue architecture across millimeter to nanometer scales.
  Nature Biotechnology 42.7 (2024). DOI: 10.1038/s41587-023-01911-8

• Hongcheng Mai, Jie Luo, Luciano Hoeher, Rami Al-Maskari, Izabela Horvath, Ying Chen, Florian Kofler, Marie Piraud, Johannes C. Paetzold, Jennifer Modamio, Mihail Todorov, Markus Elsner, Farida Hellal & Ali Ertürk.
  Whole-body cellular mapping in mouse using standard IgG antibodies.
  Nature Biotechnology 42.4 (2024). DOI: 10.1038/s41587-023-01846-0
  View data in WEBKNOSSOS.

• Kievits, Arent J., Duinkerken, B. H. Peter, Lane, Ryan, de Heus, Cecilia, van Beijeren Bergen en Henegouwen, Daan, Höppener, Tibbe, Wolters, Anouk H. G., Liv, Nalan, Giepmans, Ben N. G. and Hoogenboom, Jacob P..
  FAST-EM array tomography: a workflow for multibeam volume electron microscopy
  Methods in Microscopy (2024). DOI: 10.1515/mim-2024-0005

• Yan Lu, Yi Jiang, Fangfang Wang, Hao Wu & Yunfeng Hua.
  Electron Microscopic Mapping of Mitochondrial Morphology in the Cochlear Nerve Fibers.
  Journal of the Association for Research in Otolaryngology 25.4 (2024). DOI: 10.1007/s10162-024-00957-y

• Vandana Sampathkumar, Kevin P. Koster, Briana J. Carroll, S. Murray Sherman, & Narayanan Kasthuri.
  Synaptic integration of somatosensory and motor cortical inputs onto spiny projection neurons of mice caudoputamen.
  European Journal of Neuroscience 60.8 (2024). DOI: 10.1111/ejn.16538

• Angeles Salles, Emely Loscalzo, Jessica Montoya, Rosa Mendoza, Kevin M. Boergens & Cynthia F. Moss.
  Auditory processing of communication calls in interacting bats.
  Iscience 27.6 (2024). DOI: 10.1016/j.isci.2024.109872

• Wen-Qing Huang, Haibin Sheng, Haoyu Wang, Yumeng Qi, Fangfang Wang, & Yunfeng Hua.
  Volume electron microscopy reveals age-related ultrastructural differences of globular bush cell axons in mouse central auditory system.
  Neurobiology of Aging 136 (2024). DOI: 10.1016/j.neurobiolaging.2024.01.016

• Yi Jiang, Haoyu Wang, Kevin Boergens, Norman Rzepka, Fangfang Wang, & Yunfeng Hua.
  Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos.
  bioRxiv (2024). DOI: 10.1101/2024.10.20.619271

• Yuh-Tarng Chen, Dominica de Thomas Wagner, Alastair J. Loutit, Ali Nourizonoz, Mary-Claude Croisier-Coeytaux, Jérôme Blanc, Graham Knott, Kuo-Sheng Lee, & Daniel Huber.
  Lamellar Schwann cells in the Pacinian corpuscle potentiate vibration perception.
  bioRxiv (2024). DOI: 10.1101/2024.08.23.609459

• Rafael Luján, Marta Turegano-Lopez, Carolina Aguado, & Angel Merchan-Perez.
  Two- and three-dimensional electron microscopy techniques: powerful tools for studying the brain under physiological and pathological conditions.
  Advanced Technology in Neuroscience 1.2 (2024). DOI: 10.4103/ATN.ATN-D-24-00009

• Nare Karagulyan, Maja Überegger, Yumeng Qi, Norbert Babai, Florian Hofer, Lejo Johnson Chacko, Fangfang Wang, Maria Luque, Rudolf Glueckert, Anneliese Schrott-Fischer, Yunfeng Hua, Tobias Moser, & Christine Bandtlow.
  Probing the role of synaptic adhesion molecule RTN4RL2 in setting up cochlear connectivity.
  bioRxiv (2024). DOI: 10.1101/2024.09.16.613011

• Kristina D Micheva, Anish K Simhal, Jenna Schardt, Stephen J Smith, Richard J Weinberg, & Scott F Owen.
  Data-driven synapse classification reveals a logic of glutamate receptor composition.
  bioRxiv (2024). DOI: 10.1101/2024.12.11.628056

• Guangmei Liu, Shruthi Bandyadka, & Kimberly McCall.
  Protocol to analyze 3D neurodegenerative vacuoles in Drosophila melanogaster.
  STAR protocols 5.2 (2024). DOI: 10.1016/j.xpro.2024.103017

• Jakob Reichmann, Jonas Franz, Marina Eckermann, Katja Schulz, Brit Mollenhauer, Christine Stadelmann, & Tim Salditt.
  3D imaging of neuronal inclusions and protein aggregates in human neurodegeneration by multiscale X-ray phase-contrast tomography.
  medRxiv (2024). DOI: 10.1101/2024.03.26.24304193

• Tay Won Shin, Hao Wang, Chi Zhang, Bobae An, Yangning Lu, Elizabeth Zhang, Xiaotang Lu, Emmanouil D. Karagiannis, Jeong Seuk Kang, Amauche Emenari, Panagiotis Symvoulidis, Shoh Asano, Leanne Lin, Emma K. Costa; IMAXT Grand Challenge Consortium, Adam H. Marblestone, Narayanan Kasthuri, Li-Huei Tsai, Edward S. Boyden.
  Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues.
  bioRxiv (2024). DOI: 10.1101/2024.03.07.583776

• Carina C. Theobald, Ahmadali Lotfinia, Jan A. Knobloch, Yasser Medlej, David R. Stevens & Marcel A. Lauterbach.
  Distribution of spine classes shows intra-neuronal dendritic heterogeneity in mouse cortex.
  Neurophotonics, Vol. 12, Issue 1, 015001. SPIE (2024). DOI: 1.NPh.12.1.015001

• Norman Rzepka.
  Next-generation file formats (NGFF), RFC 2: Specification for using Zarr v3 in OME-Zarr.
  NGFF RFC 2 (2024).

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.