Stephan Saalfeld

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Pavel TomancakResearch Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics in DresdenVerified email at mpi-cbg.de
Stephan PreibischHHMI Janelia & BIMSB, MDCVerified email at janelia.hhmi.org
Albert CardonaHHMI JaneliaVerified email at janelia.hhmi.org
Johannes SchindelinVerified email at wisc.edu
Mark Longair(Previously) Postdoctoral researcher, Institute of Neuroinformatics, Uni / ETH ZürichVerified email at longair.net
Ignacio Arganda-CarrerasIkerbasque Associate Researcher at University of the Basque Country and DIPCVerified email at ehu.eus
Kevin EliceiriDirector, Laboratory for Optical and Computational Instrumentation, University of Wisconsin at MadisonVerified email at wisc.edu
Jean-Yves TinevezResearch engineer, Institut Pasteur, Paris, FranceVerified email at pasteur.fr
Verena KaynigHarvard UniversityVerified email at seas.harvard.edu
Curtis RuedenUniversity of Wisconsin-MadisonVerified email at wisc.edu
John BogovicHHMI Janelia Research CampusVerified email at janelia.hhmi.org
Philipp HanslovskyBioinformatics Specialist, HHMI JaneliaVerified email at janelia.hhmi.org
Jan FunkeHHMI Janelia Research CampusVerified email at janelia.hhmi.org
Andrew ChampionGraduate Scholar, HHMI Janelia Research Campus & University of CambridgeVerified email at janelia.hhmi.org
Stephan GerhardCEO, Unidesign Solutions GmbHVerified email at unidesign.solutions
Khaled KhairyHoward Hughes Medical InstituteVerified email at janelia.hhmi.org
Rodney DouglasProfessor of Computational NeuroscienceVerified email at ini.phys.ethz.ch
Helena JamborTU DresdenVerified email at tu-dresden.de
Casey M Schneider-MizellAllen Institute for Brain ScienceVerified email at alleninstitute.org
Torsten RohlfingGoogle LLCVerified email at ieee.org

Stephan Saalfeld

HHMI Janelia Research Campus

Verified email at janelia.hhmi.org - Homepage

Biomedical Image Analysis Computer Vision Machine Learning


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Fiji: an open-source platform for biological-image analysis J Schindelin, I Arganda-Carreras, E Frise, V Kaynig, M Longair, T Pietzsch, ... Nature Methods 9 (7), 676-682, 2012	28914	2012
Globally optimal stitching of tiled 3D microscopic image acquisitions S Preibisch, S Saalfeld, P Tomancak Bioinformatics 25 (11), 1463-1465, 2009	1555	2009
TrakEM2 software for neural circuit reconstruction A Cardona, S Saalfeld, J Schindelin, I Arganda-Carreras, S Preibisch, ... PLoS One 7 (6), e38011, 2012	641	2012
A complete electron microscopy volume of the brain of adult Drosophila melanogaster Z Zheng, JS Lauritzen, E Perlman, CG Robinson, M Nichols, D Milkie, ... Cell 174 (3), 730-743. e22, 2018	380	2018
An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy A Cardona, S Saalfeld, S Preibisch, B Schmid, A Cheng, J Pulokas, ... PLoS Biology 8 (10), e1000502, 2010	341	2010
Software for bead-based registration of selective plane illumination microscopy data S Preibisch, S Saalfeld, J Schindelin, P Tomancak Nature methods 7 (6), 418-419, 2010	341	2010
CATMAID: collaborative annotation toolkit for massive amounts of image data S Saalfeld, A Cardona, V Hartenstein, P Tomančák Bioinformatics 25 (15), 1984-1986, 2009	239	2009
Elastic volume reconstruction from series of ultra-thin microscopy sections S Saalfeld, R Fetter, A Cardona, P Tomancak Nature Methods 9 (7), 717-720, 2012	228	2012
Quantitative neuroanatomy for connectomics in Drosophila CM Schneider-Mizell, S Gerhard, M Longair, T Kazimiers, F Li, MF Zwart, ... Elife 5, e12059, 2016	209	2016
Whole-brain serial-section electron microscopy in larval zebrafish DGC Hildebrand, M Cicconet, RM Torres, W Choi, TM Quan, J Moon, ... Nature 545 (7654), 345-349, 2017	193	2017
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution R Gao, SM Asano, S Upadhyayula, I Pisarev, DE Milkie, TL Liu, V Singh, ... Science 363 (6424), eaau8302, 2019	162	2019
BigDataViewer: visualization and processing for large image data sets T Pietzsch, S Saalfeld, S Preibisch, P Tomancak Nature Methods 12 (6), 481-483, 2015	157	2015
A Connectome and Analysis of the Adult Drosophila Central Brain LK Scheffer, CS Xu, M Januszewski, Z Lu, S Takemura, KJ Hayworth, ... bioRxiv, 2020	147*	2020
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets S Saalfeld, A Cardona, V Hartenstein, P Tomančák Bioinformatics 26 (12), i57-i63, 2010	130	2010
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development H Jambor, V Surendranath, AT Kalinka, P Mejstrik, S Saalfeld, ... eLife 4, e05003, 2015	104	2015
Large scale image segmentation with structured loss based deep learning for connectome reconstruction J Funke, F Tschopp, W Grisaitis, A Sheridan, C Singh, S Saalfeld, ... IEEE transactions on pattern analysis and machine intelligence 41 (7), 1669-1680, 2018	102*	2018
ImgLib2—generic image processing in Java T Pietzsch, S Preibisch, P Tomančák, S Saalfeld Bioinformatics 28 (22), 3009–3011, 2012	97	2012
Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts A Cardona, S Saalfeld, I Arganda, W Pereanu, J Schindelin, V Hartenstein The Journal of Neuroscience 30 (22), 7538-7553, 2010	62	2010
Robust registration of calcium images by learned contrast synthesis JA Bogovic, P Hanslovsky, A Wong, S Saalfeld 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), 1123-1126, 2016	38	2016
To the cloud! A grassroots proposal to accelerate brain science discovery JT Vogelstein, B Mensh, M Häusser, N Spruston, AC Evans, K Kording, ... Neuron 92 (3), 622-627, 2016	37	2016

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