Browse by Research Team

Article

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F., Neuschulz, A., Junker, J.P., Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Best practice standards for circular RNA research.
Nielsen, A.F., Bindereif, A., Bozzoni, I., Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S., Legnini, I., Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J., Preibisch, S., Rajewsky, N., Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F., Dos Santos, N., Contzen, J., Stachelscheid, H., Costa, E.T., Mergenthaler, P. and Preibisch, S.
Bioinformatics 37 (18): 3088-3090. 15 September 2021

Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N., Preusser, F., Wisniewski, J., Yaniv, Z., Desai, R.A., Woehler, A. and Preibisch, S.
Biomedical Optics Express 12 (4): 2186-2203. 1 April 2021

Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer.
Le Poul, Y., Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., Osipova, E., Museridze, M., Dharmadhikari, D., Murphy, E., Rohs, R., Preibisch, S., Prud'homme, B. and Gompel, N.
Science Advances 6 (49): eabe2955. 2 December 2020

Resolving titin's lifecycle and the spatial organization of protein turnover in mouse cardiomyocytes.
Rudolph, F., Hüttemeister, J., da Silva Lopes, K., Jüttner, R., Yu, L., Bergmann, N., Friedrich, D., Preibisch, S., Wagner, E., Lehnart, S.E., Gregorio, C.C. and Gotthardt, M.
Proceedings of the National Academy of Sciences of the United States of America 116 (50): 25126-25136. 10 December 2019

Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency.
Friedrich, D., Friedel, L., Finzel, A., Herrmann, A., Preibisch, S. and Loewer, A.
Molecular Systems Biology 15 (12): e9068. 1 December 2019

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D., Rojas Rusak, F., Preusser, F., Tillberg, P., Randel, N., Chhetri, R.K., Cardona, A., Keller, P.J., Harz, H., Leonhardt, H., Treier, M. and Preibisch, S.
Nature Methods 16 (9): 870-874. September 2019

Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I., Bröhl, D., Zyrianova, T., Isomura, A., Czajkowski, M.T., Kapoor, V., Griger, J., Ruffault, P.L., Mademtzoglou, D., Zammit, P.S., Wunderlich, T., Spuler, S., Kühn, R., Preibisch, S., Wolf, J., Kageyama, R. and Birchmeier, C.
Genes & Development 33 (9-10): 524-535. 1 May 2019

MTrack: automated detection, tracking, and analysis of dynamic microtubules.
Kapoor, V., Hirst, W.G., Hentschel, C., Preibisch, S. and Reber, S.
Scientific Reports 9 (1): 3794. 7 March 2019

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.
Vladimirov, N., Wang, C., Höckendorf, B., Pujala, A., Tanimoto, M., Mu, Y., Yang, C.T., Wittenbach, J.D., Freeman, J., Preibisch, S., Koyama, M., Keller, P.J. and Ahrens, M.B.
Nature Methods 15 (12): 1117-1125. December 2018

DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.
La Fortezza, M., Grigolon, G., Cosolo, A., Pindyurin, A., Breimann, L., Blum, H., van Steensel, B. and Classen, A.K.
Epigenetics & Chromatin 11 (1): 27. 5 June 2018

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb.
Wolff, C., Tinevez, J.Y., Pietzsch, T., Stamataki, E., Harich, B., Guignard, L., Preibisch, S., Shorte, S., Keller, P.J., Tomancak, P. and Pavlopoulos, A.
eLife 7 : e34410. 29 March 2018

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells.
Mönke, G., Cristiano, E., Finzel, A., Friedrich, D., Herzel, H., Falcke, M. and Loewer, A.
Scientific Reports 7 : 46571. 18 April 2017

Autoionization in time-dependent density-functional theory.
Kapoor, V.
Physical Review A 93 (6): 063408. 8 June 2016

Using light sheet fluorescence microscopy to image zebrafish eye development.
Icha, J., Schmied, C., Sidhaye, J., Tomancak, P., Preibisch, S. and Norden, C.
Journal of Visualized Experiments 2016 (110): e53966. 10 April 2016

An automated workflow for parallel processing of large multiview SPIM recordings.
Schmied, C., Steinbach, P., Pietzsch, T., Preibisch, S. and Tomancak, P.
Bioinformatics 32 (7): 1112-1114. 1 April 2016

Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.
Smith, C.S., Preibisch, S., Joseph, A., Abrahamsson, S., Rieger, B., Myers, E., Singer, R.H. and Grunwald, D.
Journal of Cell Biology 209 (4): 609-619. 25 May 2015

Bioimage informatics in the context of drosophila research.
Jug, F., Pietzsch, T., Preibisch, S. and Tomancak, P.
Methods 68 (1): 60-73. 15 June 2014

Efficient Bayesian-based multiview deconvolution.
Preibisch, S., Amat, F., Stamataki, E., Sarov, M., Singer, R.H., Myers, E. and Tomancak, P.
Nature Methods 11 (6): 645-648. June 2014

ImgLib2-generic image processing in Java.
Pietzsch, T., Preibisch, S., Tomancak, P. and Saalfeld, S.
Bioinformatics 28 (22): 3009-3011. 15 November 2012

Fiji: an open-source platform for biological-image analysis.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.Y., White, D.J., Hartenstein, V., Eliceiri, K., Tomancak, P. and Cardona, A.
Nature Methods 9 (7): 676-682. July 2012

TrakEM2 software for neural circuit reconstruction.
Cardona, A., Saalfeld, S., Schindelin, J., Arganda-Carreras, I., Preibisch, S., Longair, M., Tomancak, P., Hartenstein, V. and Douglas, R.J.
PLoS ONE 7 (6): e38011. 19 June 2012

Restoration of uneven illumination in light sheet microscopy images.
Uddin, M.S., Lee, H.K., Preibisch, S. and Tomancak, P.
Microscopy and Microanalysis 17 (4): 607-613. August 2011

Gene expression divergence recapitulates the developmental hourglass model.
Kalinka, A.T., Varga, K.M., Gerrard, D.T., Preibisch, S., Corcoran, D.L., Jarrells, J., Ohler, U., Bergman, C.M. and Tomancak, P.
Nature 468 (7325): 811-814. 9 December 2010

Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
Carrillo Oesterreich, F., Preibisch, S. and Neugebauer, K.M.
Molecular Cell 40 (4): 571-581. 24 November 2010

Planar cell polarity signalling regulates cell adhesion properties in progenitors of the zebrafish laterality organ.
Oteiza, P., Koeppen, M., Krieg, M., Pulgar, E., Farias, C., Melo, C., Preibisch, S., Mueller, D., Tada, M., Hartel, S., Heisenberg, C.P. and Concha, M.L.
Development 137 (20): 3459-3468. 15 October 2010

An integrated micro- and macroarchitectural analysis of the drosophila brain by computer-assisted serial section electron microscopy.
Cardona, A., Saalfeld, S., Preibisch, S., Schmid, B., Cheng, A., Pulokas, J., Tomancak, P. and Hartenstein, V.
PLoS Biology 8 (10): e1000502. 5 October 2010

Calibration of microarray gene-expression data.
Binder, H., Preibisch, S. and Berger, H.
Methods in Molecular Biology 576 : 375-407. 2010

Globally optimal stitching of tiled 3D microscopic image acquisitions.
Preibisch, S., Saalfeld, S. and Tomancak, P.
Bioinformatics 25 (11): 1463-1465. 1 June 2009

"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures.
Binder, H., Krohn, K. and Preibisch, S.
Algorithms for Molecular Biology 3 : 11. 29 August 2008

"Hook"-calibration of GeneChip-microarrays: theory and algorithm.
Binder, H. and Preibisch, S.
Algorithms for Molecular Biology 3 : 12. 29 August 2008

GeneChip microarrays-signal intensities, RNA concentrations and probe sequences.
Binder, H. and Preibisch, S.
Journal Of Physics: Condensed Matter 18 (18): S537-S566. 10 May 2006

Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.
Binder, H., Preibisch, S. and Kirsten, T.
Langmuir 21 (20): 9287-9302. 27 September 2005

Specific and nonspecific hybridization of oligonucleotide probes on microarrays.
Binder, H. and Preibisch, S.
Biophysical Journal 89 (1): 337-352. July 2005

Book Section

Image processing and analysis of light sheet microscopy data.
Jain, A., Ulman, V., Krumnikl, M., Pietzsch, T., Preibisch, S. and Tomančák, P.
In: Light Sheet Fluorescence Microscopy. Wiley‐VCH GmbH, Weinheim, Germany, 203-229. ISBN 9783527341351 18 March 2024

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P., Epstein, L. and Guignard, L.
In: Cell Movement in Health and Disease. Academic Press, London, 341-361. ISBN 978-0-323-90195-6 2022

Review

Light sheet fluorescence microscopy.
Stelzer, E.H.K., Strobl, F., Chang, B.J., Preusser, F., Preibisch, S., McDole, K. and Fiolka, R.
Nature Reviews Methods Primers 1 (1): 73. 3 November 2021

Light-microscopy methods in C. elegans research.
Breimann, L., Preusser, F. and Preibisch, S.
Current Opinion in Systems Biology 13 : 82-92. February 2019

Letter

BigDataViewer: visualization and processing for large image data sets.
Pietzsch, T., Saalfeld, S., Preibisch, S. and Tomancak, P.
Nature Methods 12 (6): 481-483. 28 May 2015

OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone, P.G., Schindelin, J., Stuyvenberg, L., Preibisch, S., Weber, M., Eliceiri, K.W., Huisken, J. and Tomancak, P.
Nature Methods 10 (7): 598-599. July 2013

Software for bead-based registration of selective plane illumination microscopy data.
Preibisch, S., Saalfeld, S., Schindelin, J. and Tomancak, P.
Nature Methods 7 (6): 418-419. June 2010

Editorial

The author file: Stephan Preibisch.
Marx, V.
Nature Methods 16 (9): 793. September 2019

Preprint

Scalable image-based visualization and alignment of spatial transcriptomics datasets.
Preibisch, S., Innerberger, M., León-Periñán, D., Karaiskos, N. and Rajewsky, N.
bioRxiv : 2021.12.07.471629v3. 7 October 2024

Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos.
Breimann, L., Bahry, E., Zouinkhi, M., Kolyvanov, K., Street, L.A., Preibisch, S. and Ercan, S.
bioRxiv : 2024.05.15.594414. 16 May 2024

Visualizing sarcomere and cellular dynamics in skeletal muscle to improve cell therapies.
Hüttemeister, J., Rudolph, F., Radke, M.H., Fink, C., Friedrich, D., Preibisch, S., Falcke, M., Wagner, E., Lehnart, S.E. and Gotthardt, M.
bioRxiv : 2024.02.01.578471. 7 February 2024

Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis.
Le Poul, Y., Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., Osipova, E., Museridze, M., Dharmadhikari, D., Murphy, E., Rohs, R., Preibisch, S., Prud'homme, B. and Gompel, N.
bioRxiv : 2020.06.24.169748. 25 June 2020