References

The following publications used WEBKNOSSOS for their work. Please get in touch with us if your publication is missing.

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    • 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,
      2023


    • Distinctive 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. Wong

    • 10.1016/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. Kuan

    • 0.48550/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 Lee

    • 10.1038/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 Guilmi

    • 10.3389/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.

    • 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

    • 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

    • 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

    • 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

    • 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

    • 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

    • 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

    • 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