| layout | title | permalink | weight |
|---|---|---|---|
page |
Publications |
/publications/ |
1 |
journal publication, review, conference proceeding, book chapter; * indicates co-first authorship
Carlas Smith*, Stephan Preibisch*, Aviva Joseph, Bernd Rieger, Sjoerd Stallinga, Eugene Myers, Robert H. Singer, David Grunwald (2015)
Nuclear accessibility of β-actin mRNA measured by 3D single-molecule real time (3D-SMRT) microscopy
Journal of Cell Biology 209(4), 609-619;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H. Singer, Eugene Myers, Pavel Tomancak (2014)
Efficient Bayesian-based multiview deconvolution
Nature Methods 11(6), 645-648;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
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, Albert Cardona (2012)
Fiji - an open source platform for biological image analysis
Nature Methods 9(7), 676-682;
Link to Paper{:target="_blank"}
Stephan Preibisch*, Stephan Saalfeld*, Johannes Schindelin, Pavel Tomancak (2010)
Software for bead-based registration of selective plane illumination microscopy data
Nature Methods 7(6), 418-419;
Link to Paper{:target="_blank"}
Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak (2009)
Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions
Bioinformatics 25(11), 1463-1465;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Laura Breimann, Friedrich Preusser, Stephan Preibisch (2018) **Light-microscopy methods in *C. elegans* research** *Current Opinion in Systems Biology* [Link to paper](https://www.sciencedirect.com/science/article/pii/S2452310018300842?via%3Dihub){:target="_blank"}
Nikita Vladimirov, Chen Wang, Burkhard Höckendorf, Avinash Pujala, Masashi Tanimoto, Yu Mu, Chao-Tsung Yang, Jason D. Wittenbach, Jeremy Freeman, Stephan Preibisch, Minoru Koyama, Philipp J. Keller & Misha B. Ahrens (2018)
Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function
Nature Methods
PDF, read-only{:target="_blank"}
Varun Kapoor, William G Hirst, Christoph Hentschel, Stephan Preibisch, Simone Reber (2018)
MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules
bioRxiv
Link to Paper{:target="_blank"}
David Hörl, Fabio Rojas Rusak, Friedrich Preusser, Paul Tillberg, Nadine Randel, Raghav K. Chhetri, Albert Cardona, Philipp J. Keller, Hartmann Harz, Heinrich Leonhardt, Mathias Treier, Stephan Preibisch (2018)
BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples.
bioRxiv
Link to Paper{:target="_blank"}
Carsten Wolff, Jean-Yves Tinevez, Tobias Pietzsch, Evangelia Stamataki, Benjamin Harich, Stephan Preibisch, Spencer Shorte, Philipp J. Keller, Pavel Tomancak, Anastasios Pavlopoulos (2017)
Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking
bioRxiv 112623;
Link to Paper{:target="_blank"}
Jaroslav Icha, Christopher Schmied, Jaydeep Sidhaye, Pavel Tomancak, Stephan Preibisch, Caren Norden (2016)
Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development
Journal of Visualized Experiments (JoVE) 110:e53966;
Link to Paper{:target="_blank"}
Christopher Schmied, Peter Steinbach, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak (2016)
An automated workflow for parallel processing of large multiview SPIM recordings
Bioinformatics 32(7), 1112-1114;
Link to Paper{:target="_blank"}
Carlas Smith*, Stephan Preibisch*, Aviva Joseph, Bernd Rieger, Sjoerd Stallinga, Eugene Myers, Robert H. Singer, David Grunwald (2015)
Nuclear accessibility of β-actin mRNA measured by 3D single-molecule real time (3D-SMRT) microscopy
Journal of Cell Biology 209(4), 609-619;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch, Pavel Tomancak (2015)
BigDataViewer: visualization and processing for large image data sets
Nature Methods 12(6), 481-483;
Link to Paper{:target="_blank"}
Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H. Singer, Eugene Myers, Pavel Tomancak (2014)
Efficient Bayesian-based multiview deconvolution
Nature Methods 11(6), 645-648;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak (2014) **Bioimage Informatics in the context of Drosophila research** *Methods* **68**(1), 60-73; [Link to Paper](https://www.sciencedirect.com/science/article/pii/S1046202314001480){:target="_blank"}
Peter Pitrone, Johannes Schindelin, Luke Stuyvenberg, Stephan Preibisch, Michael Weber, Kevin W. Eliceiri, Jan Huisken, Pavel Tomancak (2013)
OpenSPIM - an open access platform for light sheet microscopy
Nature Methods 10(7), 598-599;
Link to Paper{:target="_blank"}
Tobias Pietzsch*, Stephan Preibisch*, Pavel Tomancak, Stephan Saalfeld* (2012)
ImgLib2 - Generic image processing in Java
Bioinformatics 28(22), 3009-3011;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
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, Albert Cardona (2012)
Fiji - an open source platform for biological image analysis
Nature Methods 9(7), 676-682;
Link to Paper{:target="_blank"}
Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney Douglas (2012)
TrakEM2 software for neural circuit reconstruction
PLoS One 7(6), e38011;
Link to Paper{:target="_blank"}
Mohammad Shorif Uddin, Hwee Kuan Lee, Stephan Preibisch, Pavel Tomancak (2011)
Restoration of Uneven Illumination in Light Sheet Microscopy Images
Microscopy and Microanalysis 17(4), 607-613;
Link to Paper{:target="_blank"}
Stephan Preibisch*, Stephan Saalfeld*, Johannes Schindelin, Pavel Tomancak (2010)
Software for bead-based registration of selective plane illumination microscopy data
Nature Methods 7(6), 418-419;
Link to Paper{:target="_blank"}
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 model
Nature 468(7325), 811-814;
Link to Paper{:target="_blank"}
Fernando-Carrillo Österreich, Stephan Preibisch, Karla Neugebauer (2010)
Global analysis of nascent RNA identifies splicing-specific transcriptional pausing in terminal exons
Molecular Cell 40(4), 571-581;
Link to Paper{:target="_blank"}
Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Pavel Tomancak, Anchi Cheng, Jim Pulokas, 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;
Link to Paper{:target="_blank"}
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;
Link to Paper{:target="_blank"}
Stephan Preibisch, Pavel Tomancak, Stephan Saalfeld (2010) **Into ImgLib – Generic Image Processing in Java** in *ImageJ User and Developer Conference 2010*, 72-76; [Link to Website](https://imagejconf.tudor.lu/archive/imagej-user-and-developer-conference-2010){:target="_blank"}, [PDF]({{ site.baseurl }}/assets/imagejpaper2010.pdf){:target="_blank"}
Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak (2009)
Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions
Bioinformatics 25(11), 1463-1465;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Stephan Preibisch, Stephan Saalfeld, Torsten Rohlfing, Pavel Tomancak (2009) **Bead-based mosaicing of single plane illumination microscopy images using geometric local descriptor matching** in *SPIE Medical Imaging 2009: Image Processing* **7259**(72592S), 1-10; [Link to Paper](https://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1335480){:target="_blank"}, [PDF]({{ site.baseurl }}/assets/spie2009_beads.pdf){:target="_blank"}
Hans Binder, Stephan Preibisch, Hilmar Berger (2009) **Calibration of microarray gene-expression data** in *Methods in Molecular Medicine: Cancer gene profiling, Methods and Protocols*, ISBN:978-1-934115-76-3; [Link to Book](https://www.springer.com/us/book/9781934115763){:target="_blank"}
Stephan Preibisch, Radoslav Ejsmont, Torsten Rohlfing, Pavel Tomancak (2008) **Towards Digital Representation of Drosophila Embryogenesis** in *IEEE Biomedical Imaging: From Nano to Macro* **5**, 324-327; [Link to Paper](https://ieeexplore.ieee.org/document/4540998/?arnumber=4540998){:target="_blank"}, [PDF]({{ site.baseurl }}/assets/ISBI_2008.pdf){:target="_blank"}
Stephan Preibisch, Torsten Rohlfing, Michael Hasak, Pavel Tomancak (2008) **Mosaicing of Single Plane Illumination Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion** in *SPIE Medical Imaging 2008: Image Processing* **6914**(69140E), 1-8; [Link to Paper](https://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=827745){:target="_blank"}, [PDF]({{ site.baseurl }}/assets/spim_congeal_2008.pdf){:target="_blank"}
Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak (2008) **Fast Stitching of Large 3D Biological Datasets** in *ImageJ User and Developer Conference 2008*, 72-76; [Link to Website](https://imagejconf.tudor.lu/archive/imagej-user-and-developer-conference-2008){:target="_blank"}, [PDF]({{ site.baseurl }}/assets/imagejpaper2008.pdf){:target="_blank"}
Hans Binder, Stephan Preibisch (2008)
"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
Algorithms for Molecular Biology 3:11;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Hans Binder, Knut Krohn, Stephan Preibisch (2008)
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Algorithms for Molecular Biology 3:12;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Hans Binder, Stephan Preibisch (2006)
GeneChip microarrays-signal intensities, RNA concentrations and probe sequences.
Journal of Physics: Condensed Matter 18(18), 537-566;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Hans Binder, Stephan Preibisch (2005).
Specific and non specific hybridization of oglionucleotide probes on microarrays.
Biophysical Journal 89(1), 337-352;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}
Hans Binder, Stephan Preibisch, Toralf Kirsten (2005).
Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.
Langmuir 21(20), 9287-9302;
Link to Paper{:target="_blank"},
PDF{:target="_blank"}