Contact

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden, Germany

phone +49 351 210-2753
fax+49 351 210-1389

saalfeld@mpi-cbg.de

Publications

Journal articles

Tobias Pietzsch, Stephan Preibisch, Pavel Tomančák, and Stephan Saalfeld, “ImgLib2—Generic Image Processing in Java,” Bioinformatics, 28(22), 3009–3011 (2012), doi:10.1093/bioinformatics/bts543. Article, corrected references

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomančák, Volker Hartenstein, and Rodney J. Douglas, “TrakEM2 Software for Neural Circuit Reconstruction,” PLoS ONE, 7(6), e38011 (2012), doi:10.1371/journal.pone.0038011. Article

Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomančák, and Albert Cardona, “Fiji: an open-source platform for biological-image analysis,” Nature Methods, 9, 676–682 (2012), doi:10.1038/nmeth.2019. Article

Stephan Saalfeld, Richard Fetter, Albert Cardona, and Pavel Tomančák, “Elastic volume reconstruction from series of ultra-thin microscopy sections,” Nature Methods, 9, 717–720 (2012), doi:10.1038/nmeth.2072. Article

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomančák, Volker Hartenstein, and Rodney J. Douglas, “TrakEM2 Software for Neural Circuit Reconstruction,” PLoS ONE, 7(6), e38011 (2012), doi:10.1371/journal.pone.0038011. Article

Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Anchi Cheng, Jim Pulokas, Pavel Tomančák, and Volker Hartenstein, “An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy,” PLoS Biology, 8(10), e1000502 (2010), doi:10.1371/journal.pbio.1000502. Article, PDF

Stephan Saalfeld, Albert Cardona, Volker Hartenstein, and Pavel Tomančák, “As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets,” Bioinformatics, 26(12), i57–i63 (2010), doi:10.1093/bioinformatics/btq219. Article, PDF

Albert Cardona, Stephan Saalfeld, Ignacio Arganda, Wayne Pereanu, Johannes Schindelin, Volker Hartenstein, “Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts,” The Journal of Neuroscience, 30(22), 7538–7553 (2010), doi:10.1523/JNEUROSCI.0186-10.2010. Abstract, PDF

Stephan Preibisch*, Stephan Saalfeld*, Johannes Schindelin, Pavel Tomančák, “Software for bead-based registration of selective plane illumination microscopy data,” Nature Methods, 7, 418–419 (2010), doi:10.1038/nmeth0610-418. Abstract, PDF

Albert Cardona, Stephan Saalfeld, Pavel Tomančák, Volker Hartenstein, “Drosophila Brain Development: Closing the Gap between a Macroarchitectural and Microarchitectural Approach,” Cold Spring Harb Symp Quant Biol., published in advance Dec 22, 2009, doi:10.1101/sqb.2009.74.037. Abstract, PDF

Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomančák, “CATMAID: Collaborative Annotation Toolkit for Massive Amounts of Image Data,” Bioinformatics, 25(19), 1984–1986 (2009). Article, PDF

Stephan Preibisch, Stephan Saalfeld, Pavel Tomančák, “Globally Optimal Stitching of Tiled 3D Microscopic Image Acquisitions,” Bioinformatics, 25(11), 1463–1465 (2009). Article, PDF

Conference proceedings

Stephan Saalfeld, Tobias Pietzsch, Pavel Tomančák, and Stephan Preibisch, “ImgLib2—Generic Image Processing in Java,” In Proceedings of the ImageJ User and Developer Conference, Mondorf-les-Bains, Luxembourg (2012).

Tobias Pietzsch, Stephan Preibisch, Pavel Tomančák, and Stephan Saalfeld, “Advanced Programming with ImgLib2,” In Proceedings of the ImageJ User and Developer Conference, Mondorf-les-Bains, Luxembourg (2012).

Stephan Preibisch, Tobias Pietzsch, Gene Myers, Pavel Tomančák, and Stephan Saalfeld, “Introduction to ImgLib2,” In Proceedings of the ImageJ User and Developer Conference, Mondorf-les-Bains, Luxembourg (2012).

Stephan Preibisch, Pavel Tomančák, and Stephan Saalfeld, “Into ImgLib—Generic Image Processing in Java,” In Proceedings of the ImageJ User and Developer Conference, Mondorf-les-Bains, Luxembourg (2010). PDF, Workshop

Stephan Preibisch, Stephan Saalfeld, Torsten Rohlfing, Pavel Tomančák, “Bead-based Mosaicing of Single Plane Illumination Microscopy Images Using Geometric Local Descriptor Matching,” In Proceedings of SPIE, 72592S (2009). PDF

Stephan Saalfeld, Pavel Tomančák, “Automatic landmark correspondence detection for ImageJ,” In Proceedings of the ImageJ User and Developer Conference, 128–133, Luxembourg (2008). PDF

Stephan Preibisch, Stephan Saalfeld, Pavel Tomančák, “Fast stitching of large 3d biological datasets,” In Proceedings of the ImageJ User and Developer Conference, 134–139, Luxembourg (2008). PDF

* co-first