Homepage of Stephan Preibisch                     

HFSP Fellow in the labs of Robert H. Singer and Eugene Myers at the Albert Einstein College and the MPI-CBG
Visiting Scientist at the HHMI Janelia Farm Research Campus

Publications

Journal Articles

First/Co-first Authorship

Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H. Singer, Eugene Myers and Pavel Tomancak (2014)
Efficient Bayesian-based multiview deconvolution
Nature Methods, doi:10.1038/nmeth.2929.
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Tobias Pietzsch*, Stephan Preibisch*, Pavel Tomancak and Stephan Saalfeld* (2012)
ImgLib2 - Generic image processing in Java
Bioinformatics 2012, 28(22), 3009-3011.
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Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin and Pavel Tomancak (2010)
Software for bead-based registration of selective plane illumination microscopy data
Nature Methods 7(6), 418-419.
Publisher Webpage, Overview Supplementary Data
Optimizer (movie)
Drosophila Embryogenesis (movie)

Stephan Preibisch, Stephan Saalfeld and Pavel Tomancak (2009)
Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions
Bioinformatics 2009, 25(11), 1463-1465.
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Other Authorships

Peter Pitrone, Johannes Schindelin, Luke Stuyvenberg, Stephan Preibisch, Michael Weber, Kevin W. Eliceiri, Jan Huisken and Pavel Tomancak (2013)
OpenSPIM - an open access platform for light sheet microscopy
Nature Methods, 10(7), 598-599.
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Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak and Albert Cardona (2012)
Fiji - an open source platform for biological image analysis
Nature Methods 9(7), 676-682.
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Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney Douglas (2012)
TrakEM2 software for neural circuit reconstruction
PLoS One 7(6), e38011.
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Mohammad Shorif Uddin, Hwee Kuan Lee, Stephan Preibisch and Pavel Tomancak (2011)
Restoration of Uneven Illumination in Light Sheet Microscopy Images
Microscopy and Microanalysis 17(4), 607-613.
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Alex Kalinka, Karolina Jastrzebowska, Dave Gerrard, Stephan Preibisch, Julia Jarrels, David Corcoran, Uwe Ohler, Casey Bergman, Pavel Tomancak (2010)
Gene expression divergence recapitulates the developmental hourglass
Nature 468(7325), 811-814.
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Fernando-Carrillo Österreich, Stephan Preibisch, Karla Neugebauer (2010)
Global analysis of nascent RNA identifies splicing-specific transcriptional pausing
Molecular Cell 40(4), 571-581.
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Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Pavel Tomancak, Anchi Cheng, Jim Pulokas, and Volker Hartenstein (2010)
An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy
PLoS Biology 8(10), e1000502.
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Pablo Oteiza, Mathias Koeppen, Michael Krieg, Eduardo Pulgar, Cecilia Farias, Cristina Melo, Stephan Preibisch, Daniel Müller, Masazumi Tada, Steffen Hartel, Carl-Philipp Heisenberg, Miguel Concha (2010)
Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ
Development 137(20), 3459-3468.
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Hans Binder and Stephan Preibisch (2008)   
"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
Algorithms for Molecular Biology 2008, 3:11.
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Hans Binder, Knut Krohn and Stephan Preibisch (2008)   
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Algorithms for Molecular Biology 2008, 3:12.
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Hans Binder and Stephan Preibisch (2006)
GeneChip microarrays-signal intensities, RNA concentrations and probe sequences.
Journal of Physics: Condensed Matter 18(18), 537-566.
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Hans Binder and Stephan Preibisch (2005).
Specific and non specific hybridization of oglionucleotide probes on microarrays.
Biophysical Journal 89(1), 337-352.
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Hans Binder, Stephan Preibisch and Toralf Kirsten (2005).
Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.
Langmuir 21(20), 9287-9302.
Publisher Webpage, PDF, Supporting Information

Conference Proceedings

Stephan Preibisch, Pavel Tomancak and Stephan Saalfeld (2010)
Into ImgLib - Generic Image Processing in Java
in Proceedings of ImageJ User and Developer Conference 2010
PDF

Stephan Preibisch, Stephan Saalfeld, Torsten Rohlfing and Pavel Tomancak (2009)
Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching
in Medical Imaging 2009: Image Processing, J. P. W. Pluim and B. M. Dawant, Eds., vol. 7259 of Proceedings of SPIE, p. 72592S, DOI:10.1117/12.812612
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Stephan Preibisch, Radoslav Ejsmont and Pavel Tomancak (2008)
Towards Digital Representation of Drosophila Embryogenesis
in Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium. 2008, pp. 324-327, IEEE Press.
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Stephan Preibisch, Torsten Rohlfing, Michael Hasak and Pavel Tomancak (2008)
Mosaicing of Single Plane Illumination Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion
in Medical Imaging 2008: Image Processing, J. M. Reinhardt and J. P. W. Pluim, Eds., 2008, vol. 6914 of Proceedings of SPIE, p. 69140E, DOI:10.1117/12.770893.
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Stephan Preibisch, Stephan Saalfeld and Pavel Tomancak (2008)
Fast Stitching of Large 3D Biological Datasets
in Proceedings of ImageJ User and Developer Conference 2008
PDF

Book Chapters

Hans Binder, Stephan Preibisch and Hilmar Berger (2009)
Calibration of microarray gene-expression data
in Methods in Molecular Medicine: Cancer gene profiling, Methods and Protocols, Vol. 576, R. Grützmann and C. Pilarsky (Eds.), ISBN: 978-1-934115-76-3
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Diploma Thesis

Stephan Preibisch (2006)
Sequenzspezifische Signalanalyse von Genexpressionsdaten
diploma thesis
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