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.
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.
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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.
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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.
bioRxiv (2022) DOI: 10.1101/2022.02.18.481045
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.
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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
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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.
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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.
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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
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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.
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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.