References
The following publications used WEBKNOSSOS for their work. Please get in touch with us if your publication is missing.
Publication
Title
Authors
DOI
Publication
Publication
Title
Title
Authors
Authors
DOI
DOI
Methods in Microscopy,2024
FAST-EM array tomography: a workflow for multibeam volume electron microscopy.
Kievits, Arent & Duinkerken, Peter & Lane, Ryan & Heus, Cecilia & Henegouwen, Daan & Höppener, Tibbe & Wolters, Anouk & Liv, Nalan & Giepmans, Ben & Hoogenboom, Jacob.
Publication
Methods in Microscopy,2024
Title
FAST-EM array tomography: a workflow for multibeam volume electron microscopy.
Authors
Kievits, Arent & Duinkerken, Peter & Lane, Ryan & Heus, Cecilia & Henegouwen, Daan & Höppener, Tibbe & Wolters, Anouk & Liv, Nalan & Giepmans, Ben & Hoogenboom, Jacob.
Frontiers in Neuroscience,2023
msemalign: a pipeline for serial section multibeam scanning electron microscopy volume alignment
Paul V. Watkins, Eric Jelli,
Kevin L. Briggman.
Publication
Frontiers in Neuroscience,2023
Title
msemalign: a pipeline for serial section multibeam scanning electron microscopy volume alignment
Authors
Paul V. Watkins, Eric Jelli,
Kevin L. Briggman.
Histochemistry and Cell Biology,2023
Online citizen science with the Zooniverse for analysis of biological volumetric data
Patricia Smith, Oliver N. F. King, Avery Pennington, Win Tun, Mark Basham, Martin L. Jones, Lucy M. Collinson, Michele C. Darrow & Helen Spiers
Publication
Histochemistry and Cell Biology,2023
Title
Online citizen science with the Zooniverse for analysis of biological volumetric data
Authors
Patricia Smith, Oliver N. F. King, Avery Pennington, Win Tun, Mark Basham, Martin L. Jones, Lucy M. Collinson, Michele C. Darrow & Helen Spiers
Neuroinformatics,2023
CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations
Laura Keto & Tiina Manninen
Publication
Neuroinformatics,2023
Title
CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations
Authors
Laura Keto & Tiina Manninen
Cell Reports,
2023Distinctive synaptic structural motifs link excitatory retinal interneurons to diverse postsynaptic partner types
Wan Qing Yu,
Rachael Swanstrom, Crystal
L. Sigulinsky, Richard
M. Ahlquist, Sharm Knecht, Bryan W. Jones, David M. Berson, Rachel O. Wong10.1016/j.celrep.2023.112006
Publication
Cell Reports,
2023
Title
Distinctive synaptic structural motifs link excitatory retinal interneurons to diverse postsynaptic partner types
Authors
Wan Qing Yu,
Rachael Swanstrom, Crystal
L. Sigulinsky, Richard
M. Ahlquist, Sharm Knecht, Bryan W. Jones, David M. Berson, Rachel O. Wong
DOI
10.1016/j.celrep.2023.112006
Nature, 2023
High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics
Kun Song, Zhihui Feng & Moritz Helmstaedter
10.1101/2022.03.30.48
6341
Publication
Nature, 2023
Title
High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics
Authors
Kun Song, Zhihui Feng & Moritz Helmstaedter
DOI
10.1101/2022.03.30.48
6341
arXiv, 2023
The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletons
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. Kuan0.48550/arXiv.2302.03 819
Publication
arXiv, 2023
Title
The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletons
Authors
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
DOI
0.48550/arXiv.2302.03 819
Nature, 2023
Structured cerebellar connectivity supports resilient pattern separation
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 Lee10.1038/s41586-022- 05471-w
Publication
Nature, 2023
Title
Structured cerebellar connectivity supports resilient pattern separation
Authors
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
DOI
10.1038/s41586-022- 05471-w
Frontiers, 2022
Volume electron microscopy reveals age-related circuit remodeling in the auditory brainstem
Daniela Chequer Charan, Yunfeng Hua, Haoyu Wang, Wenqing
Huang, Fangfang Wang, Ana Belén Elgoyhen, Kevin M Boergens, Mariano N Di Guilmi10.3389/fncel.2022.10 70438
Publication
Frontiers, 2022
Title
Volume electron microscopy reveals age-related circuit remodeling in the auditory brainstem
Authors
Daniela Chequer Charan, Yunfeng Hua, Haoyu Wang, Wenqing
Huang, Fangfang Wang, Ana Belén Elgoyhen, Kevin M Boergens, Mariano N Di Guilmi
DOI
10.3389/fncel.2022.10 70438
Science, 2022
Mutations in CCIN cause teratozoospermia and male infertility
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
10.1016/j.scib.2022.09. 026
Publication
Science, 2022
Title
Mutations in CCIN cause teratozoospermia and male infertility
Authors
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
DOI
10.1016/j.scib.2022.09. 026
Elife, 2022
Cross-modality synthesis of EM time series and live fluorescence imaging
Sahil Loomba, Jakob Straehle, Vijayan GangaSantella, A., Kolotuev, I., Kizilyaprak, C., & Bao, Z.
10.7554/eLife.77918
Publication
Elife, 2022
Title
Cross-modality synthesis of EM time series and live fluorescence imaging
Authors
Sahil Loomba, Jakob Straehle, Vijayan GangaSantella, A., Kolotuev, I., Kizilyaprak, C., & Bao, Z.
DOI
10.7554/eLife.77918
Science, 2022
Connectomic comparison of mouse and human cortex.
Sahil Loomba, Jakob Straehle, Vijayan Gangadharan, Natalie Heike, Abdelrahman Khalifa, Alessandro Motta, Niansheng Ju, Meike Sievers, Jens Gempt, Hanno S. Meyer & Moritz Helmstaedter.
Publication
Science, 2022
Title
Connectomic comparison of mouse and human cortex.
Authors
Sahil Loomba, Jakob Straehle, Vijayan Gangadharan, Natalie Heike, Abdelrahman Khalifa, Alessandro Motta, Niansheng Ju, Meike Sievers, Jens Gempt, Hanno S. Meyer & Moritz Helmstaedter.
Nature Communications, 2022
Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy.
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
Publication
Nature Communications, 2022
Title
Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy.
Authors
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
Nature, 2022
Neuropathic pain caused by miswiring and abnormal end organ targeting.
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.
Publication
Nature, 2022
Title
Neuropathic pain caused by miswiring and abnormal end organ targeting.
Authors
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.
Journal of Shanghai Jiaotong university (Medical Science), 2022
Application of three-dimensional electron microscopy to morphological study of neurons in brainstem cochlear nucleus.
Jialei Zhou, Haibin Sheng, Haoyu Wang, Yan Lu, Fangfang Wang, Hao Wu, Yunfeng Hua.
Publication
Journal of Shanghai Jiaotong university (Medical Science), 2022
Title
Application of three-dimensional electron microscopy to morphological study of neurons in brainstem cochlear nucleus.
Authors
Jialei Zhou, Haibin Sheng, Haoyu Wang, Yan Lu, Fangfang Wang, Hao Wu, Yunfeng Hua.
Frontiers, 2022
Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy.
Yuxin Zhang, Tobias Ackels, Alexandra Pacureanu, Marie-Christine Zdora, Anne Bonnin, Andreas T. Schaefer, Carles Bosch.
Publication
Frontiers, 2022
Title
Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using 2-photon, synchrotron X-ray and volume electron microscopy.
Authors
Yuxin Zhang, Tobias Ackels, Alexandra Pacureanu, Marie-Christine Zdora, Anne Bonnin, Andreas T. Schaefer, Carles Bosch.
Science, 2021
Postnatal connectomic development of inhibition in mouse barrel cortex
Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein, Kun Song, Moritz Helmstaedter
Publication
Science, 2021
Title
Postnatal connectomic development of inhibition in mouse barrel cortex
Authors
Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein, Kun Song, Moritz Helmstaedter
Cell reports, 2021
Electron Microscopic Reconstruction of Neural Circuitry in the Cochlea
Yunfeng Hua, Xu Ding, Haoyu Wang, Fangfang Wang, Yan Lu, Jakob Neef, Yunge Gao, Tobias Moser, Hao Wu
Publication
Cell reports, 2021
Title
Electron Microscopic Reconstruction of Neural Circuitry in the Cochlea
Authors
Yunfeng Hua, Xu Ding, Haoyu Wang, Fangfang Wang, Yan Lu, Jakob Neef, Yunge Gao, Tobias Moser, Hao Wu
The journal of comparative neurology, 2021
Cytoarchitecture and innervation of the mouse cochlear amplifier revealed by large‐scale volume electron microscopy
Haoyu Wang, Shengxiong Wang, Yan Lu, Ying Chen, Wenqing Huang, Miaoxin Qiu, Hao Wu, Yunfeng Hua
Publication
The journal of comparative neurology, 2021
Title
Cytoarchitecture and innervation of the mouse cochlear amplifier revealed by large‐scale volume electron microscopy
Authors
Haoyu Wang, Shengxiong Wang, Yan Lu, Ying Chen, Wenqing Huang, Miaoxin Qiu, Hao Wu, Yunfeng Hua
IEEE/ACM, 2020
Toward an Automated HPC Pipeline for Processing Large Scale ElectronMicroscopy Data
Rafael Vescovi, Hanyu Li, Jeffery Kinnison, Murat Keceli, Misha Salim, Narayanan Kasthuri, Thomas D Uram, Nicola Ferrier
Publication
IEEE/ACM, 2020
Title
Toward an Automated HPC Pipeline for Processing Large Scale ElectronMicroscopy Data
Authors
Rafael Vescovi, Hanyu Li, Jeffery Kinnison, Murat Keceli, Misha Salim, Narayanan Kasthuri, Thomas D Uram, Nicola Ferrier
PhD Thesis, 2020
Connectomic analysis of apical dendrite innervation in pyramidal neurons of mouse cerebral cortex
Ali Karimi
Publication
PhD Thesis, 2020
Title
Connectomic analysis of apical dendrite innervation in pyramidal neurons of mouse cerebral cortex
Authors
Ali Karimi
eLife, 2019
Cell-type specific innervation of cortical pyramidal cells at their apical tufts
Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter
Publication
eLife, 2019
Title
Cell-type specific innervation of cortical pyramidal cells at their apical tufts
Authors
Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter
Science, 2019
Dense connectomic reconstruction in layer 4 of the somatosensory cortex
Alessandro Motta, Manuel Berning, Kevin M Boergens, Benedikt Staffler, Marcel Beining, Sahil Loomba, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter
Publication
Science, 2019
Title
Dense connectomic reconstruction in layer 4 of the somatosensory cortex
Authors
Alessandro Motta, Manuel Berning, Kevin M Boergens, Benedikt Staffler, Marcel Beining, Sahil Loomba, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter
PhD Thesis, 2019
Machine Learning for Connectomics
Benedikt Staffler
Publication
PhD Thesis, 2019
Title
Machine Learning for Connectomics
Authors
Benedikt Staffler
eLife, 2019
Evolution of neuronal anatomy and circuitry in two highly divergent nematode species
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
Publication
eLife, 2019
Title
Evolution of neuronal anatomy and circuitry in two highly divergent nematode species
Authors
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
PLOS ONE, 2018
Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset
Kevin M. Boergens, Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst
Publication
PLOS ONE, 2018
Title
Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset
Authors
Kevin M. Boergens, Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst
eLife, 2018
FluoEM, virtual labeling of axons in threedimensional electron microscopy data for long-range connectomics
Florian Drawitsch, Ali Karimi, Kevin M Boergens, Moritz Helmstaedter
Publication
eLife, 2018
Title
FluoEM, virtual labeling of axons in threedimensional electron microscopy data for long-range connectomics
Authors
Florian Drawitsch, Ali Karimi, Kevin M Boergens, Moritz Helmstaedter
PhD Thesis, 2018
Connectomic analysis of mouse barrel cortex and fly optic lobe
Kevin M Boergens
Publication
PhD Thesis, 2018
Title
Connectomic analysis of mouse barrel cortex and fly optic lobe
Authors
Kevin M Boergens
PhD Thesis, 2018
Large-scale circuit reconstruction in medial entorhinal cortex
Helene Schmidt-Helmstaedter
Publication
PhD Thesis, 2018
Title
Large-scale circuit reconstruction in medial entorhinal cortex
Authors
Helene Schmidt-Helmstaedter
PhD Thesis, 2018
Connectomic analysis of the input to the principal cells of the mammalian cerebralcortex
Philip Laserstein
Publication
PhD Thesis, 2018
Title
Connectomic analysis of the input to the principal cells of the mammalian cerebralcortex
Authors
Philip Laserstein
eLife, 2018
Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit
Eliot Dow, Adrian Jacobo, Sajjad Hossain, Kimberly Siletti, A J Hudspeth
Publication
eLife, 2018
Title
Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit
Authors
Eliot Dow, Adrian Jacobo, Sajjad Hossain, Kimberly Siletti, A J Hudspeth
Nature Methods, 2017
webKnossos: efficient online 3D data annotation for connectomics
Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler, Helmstaedter
Publication
Nature Methods, 2017
Title
webKnossos: efficient online 3D data annotation for connectomics
Authors
Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler, Helmstaedter
Nature, 2017
Axonal synapse sorting in medial entorhinal cortex
Helene Schmidt, Anjali Gour, Jakob Straehle, Kevin M Boergens, Michael Brecht, Moritz Helmstaedter
Publication
Nature, 2017
Title
Axonal synapse sorting in medial entorhinal cortex
Authors
Helene Schmidt, Anjali Gour, Jakob Straehle, Kevin M Boergens, Michael Brecht, Moritz Helmstaedter
eLife, 2017
SynEM, automated synapse detection for connectomics
Benedikt Staffler, Manuel Berning, Kevin M Boergens, Anjali Gour, Patrick van der Smagt, Moritz Helmstaedter
Publication
eLife, 2017
Title
SynEM, automated synapse detection for connectomics
Authors
Benedikt Staffler, Manuel Berning, Kevin M Boergens, Anjali Gour, Patrick van der Smagt, Moritz Helmstaedter
Current Opinion in Insect Science, 2017
Learning from connectomics on the fly
Philipp Schlegel, Marta Costa, Gregory SXE Jefferis
Publication
Current Opinion in Insect Science, 2017
Title
Learning from connectomics on the fly
Authors
Philipp Schlegel, Marta Costa, Gregory SXE Jefferis
Neuron, 2015
SegEM: Efficient Image Analysis for High-Resolution Connectomics
Manuel Berning, Kevin M Boergens, Moritz Helmstaedter
Publication
Neuron, 2015
Title
SegEM: Efficient Image Analysis for High-Resolution Connectomics
Authors
Manuel Berning, Kevin M Boergens, Moritz Helmstaedter