Stephan Saalfeld

ORCID

Publication Activity (10 Years)

Years Active: 2015-2023
Publications (10 Years): 25

Top Venues

Nature methods

eLife

bioRxiv : the preprint server for biology

Histochemistry and cell biology

Howard Hughes Medical Institute Janelia Research Campus

Technische Universität Dresden Fakultät Informatik (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Howard Hughes Medical Institute Janelia Research Campus Dec 1o 2013

United States

Group Leader

Education History

Technische Universität Dresden Fakultät Informatik - Feb 25o 2013

Germany

PHD

Publications

Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jordão Bragantini, Jackson M Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Buğra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas J Schaub, Hythem Sidky, Ahmet Can Solak, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Isaac Virshup, Petr Walczysko, Alan M Watson, Erin Weisbart, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Beth A Cimini, Nils Gehlenborg, Muzlifah A Haniffa, Nathan A Hotaling, Shuichi Onami, Loïc Alain Royer, Stephan Saalfeld, Oliver Stegle, Fabian Joachim Theis, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and cell biology (2023)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jackson M Brown, Jean-Marie Burel, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Melissa Linkert, Dominik Lindner, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Matthew McCormick, Khaled Mohamed, William Moore, Buğra Özdemir, Constantin Pape, Lucas Pelkmans, Martin Prete, Tobias Pietzsch, Stephan Preibisch, Norman Rzepka, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Petr Walczysko, Alan M Watson, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Muzlifah A Haniffa, Stephan Saalfeld, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv : the preprint server for biology (2023)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jackson M Brown, Jean-Marie Burel, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Melissa Linkert, Dominik Lindner, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Matthew McCormick, Khaled Mohamed, William Moore, Buğra Özdemir, Constantin Pape, Lucas Pelkmans, Martin Prete, Tobias Pietzsch, Stephan Preibisch, Norman Rzepka, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Petr Walczysko, Alan M Watson, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Muzlifah A Haniffa, Stephan Saalfeld, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv : the preprint server for biology (2023)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jackson M Brown, Jean-Marie Burel, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Melissa Linkert, Dominik Lindner, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Matthew McCormick, Khaled Mohamed, William Moore, Buğra Özdemir, Constantin Pape, Lucas Pelkmans, Martin Prete, Tobias Pietzsch, Stephan Preibisch, Norman Rzepka, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Petr Walczysko, Alan M Watson, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Muzlifah A Haniffa, Stephan Saalfeld, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv : the preprint server for biology (2023)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jackson M Brown, Jean-Marie Burel, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Melissa Linkert, Dominik Lindner, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Matthew McCormick, Khaled Mohamed, William Moore, Buğra Özdemir, Constantin Pape, Lucas Pelkmans, Martin Prete, Tobias Pietzsch, Stephan Preibisch, Norman Rzepka, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Petr Walczysko, Alan M Watson, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Muzlifah A Haniffa, Stephan Saalfeld, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv : the preprint server for biology (2023)
Joshua L Lillvis, Hideo Otsuna, Xiaoyu Ding, Igor Pisarev, Takashi Kawase, Jennifer Colonell, Konrad Rokicki, Cristian Goina, Ruixuan Gao, Amy Hu, Kaiyu Wang, John A Bogovic, Daniel E Milkie, Linus Meienberg, Brett D Mensh, Edward S Boyden, Stephan Saalfeld, Paul W Tillberg, Barry J Dickson
Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy. eLife 11 (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Gayathri Mahalingam, Russel M Torres, Daniel Kapner, Eric T Trautman, Tim Fliss, Shamishtaa Seshamani, Eric Perlman, Rob Young, Samuel Kinn, JoAnn Buchanan, Marc M Takeno, Wenjing Yin, Daniel J Bumbarger, Ryder P Gwinn, Julie Nyhus, Ed Lein, Stephen J Smith, R Clay Reid, Khaled A Khairy, Stephan Saalfeld, Forrest C Collman, Nuno Maçarico da Costa
A scalable and modular automated pipeline for stitching of large electron microscopy datasets. eLife 11 (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods 20 (2) (2022)
Arlo Sheridan, Tri M Nguyen, Diptodip Deb, Wei-Chung Allen Lee, Stephan Saalfeld, Srinivas C Turaga, Uri Manor, Jan Funke
Local shape descriptors for neuron segmentation. Nature methods (2022)
Larissa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, John Bogovic, Nils Eckstein, Alyson Petruncio, Jody Clements, Song Pang, C Shan Xu, Jan Funke, Wyatt L Korff, Harald F Hess, Jennifer Lippincott-Schwartz, Stephan Saalfeld, Aubrey V Weigel, null null
Whole-cell organelle segmentation in volume electron microscopy. Nature 599 (7883) (2021)
Julia Buhmann, Arlo Sheridan, Caroline Malin-Mayor, Philipp Schlegel, Stephan Gerhard, Tom Kazimiers, Renate Krause, Tri M Nguyen, Larissa Heinrich, Wei-Chung Allen Lee, Rachel I Wilson, Stephan Saalfeld, Gregory S X E Jefferis, Davi D Bock, Srinivas C Turaga, Matthew Cook, Jan Funke
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set. Nature methods 18 (7) (2021)
John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Wilson Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
An unbiased template of the Drosophila brain and ventral nerve cord. PloS one 15 (12) (2020)
Louis K Scheffer, C Shan Xu, Michał Januszewski, Zhiyuan Lu, Shin-Ya Takemura, Kenneth J Hayworth, Gary B Huang, Kazunori Shinomiya, Jeremy Maitlin-Shepard, Stuart Berg, Jody Clements, Philip M Hubbard, William T Katz, Lowell Umayam, Ting Zhao, David Ackerman, Tim Blakely, John A Bogovic, Tom Dolafi, Dagmar Kainmueller, Takashi Kawase, Khaled A Khairy, Laramie Leavitt, Peter H Li, Larry Lindsey, Nicole Neubarth, Donald J Olbris, Hideo Otsuna, Eric T Trautman, Masayoshi Ito, Alexander Shakeel Bates, Jens Goldammer, Tanya Wolff, Robert R Svirskas, Philipp Schlegel, Erika Neace, Christopher J Knecht, Chelsea X Alvarado, Dennis A Bailey, Samantha Ballinger, Jolanta A Borycz, Brandon S Canino, Natasha Cheatham, Michael Cook, Marisa Dreher, Octave Duclos, Bryon Eubanks, Kelli Fairbanks, Samantha Finley, Nora Forknall, Audrey Francis, Gary Patrick Hopkins, Emily M Joyce, SungJin Kim, Nicole A Kirk, Julie Kovalyak, Shirley A Lauchie, Alanna Lohff, Charli Maldonado, Emily A Manley, Sari McLin, Caroline Mooney, Miatta Ndama, Omotara Ogundeyi, Nneoma Okeoma, Christopher Ordish, Nicholas Padilla, Christopher M Patrick, Tyler Paterson, Elliott E Phillips, Emily M Phillips, Neha Rampally, Caitlin Ribeiro, Madelaine K Robertson, Jon Thomson Rymer, Sean M Ryan, Megan Sammons, Anne K Scott, Ashley L Scott, Aya Shinomiya, Claire Smith, Kelsey Smith, Natalie L Smith, Margaret A Sobeski, Alia Suleiman, Jackie Swift, Satoko Takemura, Iris Talebi, Dorota Tarnogorska, Emily Tenshaw, Temour Tokhi, John J Walsh, Tansy Yang, Jane Anne Horne, Feng Li, Ruchi Parekh, Patricia K Rivlin, Vivek Jayaraman, Marta Costa, Gregory S X E Jefferis, Kei Ito, Stephan Saalfeld, Reed George, Ian A Meinertzhagen, Gerald M Rubin, Harald F Hess, Viren Jain, Stephen M Plaza
A connectome and analysis of the adult Drosophila central brain. eLife 9 (2020)
Ruixuan Gao, Shoh M Asano, Srigokul Upadhyayula, Igor Pisarev, Daniel E Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H Huynh, Yongxin Zhao, John A Bogovic, Jennifer Colonell, Carolyn M Ott, Christopher T Zugates, Susan J Tappan, Alfredo Rodriguez, Kishore R Mosaliganti, Shu-Hsien Sheu, H Amalia Pasolli, Song Pang, C Shan Xu, Sean G Megason, Harald F Hess, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S Boyden, Eric Betzig
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science (New York, N.Y.) 363 (6424) (2019)
Ardan Patwardhan, Robert Brandt, Sarah J Butcher, Lucy Collinson, David Gault, Kay Grünewald, Corey Hecksel, Juha T Huiskonen, Andrii Iudin, Martin L Jones, Paul K Korir, Abraham J Koster, Ingvar Lagerstedt, Catherine L Lawson, David Mastronarde, Matthew McCormick, Helen Parkinson, Peter B Rosenthal, Stephan Saalfeld, Helen R Saibil, Sirarat Sarntivijai, Irene Solanes Valero, Sriram Subramaniam, Jason R Swedlow, Ilinca Tudose, Martyn Winn, Gerard J Kleywegt
Building bridges between cellular and molecular structural biology. eLife 6 (2017)
Casey M Schneider-Mizell, Stephan Gerhard, Mark Longair, Tom Kazimiers, Feng Li, Maarten F Zwart, Andrew Champion, Frank M Midgley, Richard D Fetter, Stephan Saalfeld, Albert Cardona
Quantitative neuroanatomy for connectomics in Drosophila. eLife 5 (2016)
Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch, Pavel Tomancak
BigDataViewer: visualization and processing for large image data sets. Nature methods 12 (6) (2015)
Helena Klara Jambor, Vineeth Surendranath, Alex T Kalinka, Pavel Mejstrik, Stephan Saalfeld, Pavel Tomancak
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. eLife 4 (2015)

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Publication Activity (10 Years)

Top Topics

Top Venues

Stephan Saalfeld