Article
Innovative in vivo imaging and single cell expression from tumor bulk and corpus callosum reveal glioma stem cells with unique regulatory programs.
Dos Santos, Natalia, Aquino, Aline, Preußer, Friedrich 
ORCID: https://orcid.org/0000-0001-8231-2195, Rusak, Fabio Rojas ORCID: https://orcid.org/0000-0002-0637-9467, Jandrey, Elisa Helena Farias, Uno, Miyuki ORCID: https://orcid.org/0000-0003-2589-6432, Furuya, Tatiane Katsue, Lancellotti, Carmen Lucia Penteado, Maldaun, Marcos Vinicius Calfat, Chammas, Roger ORCID: https://orcid.org/0000-0003-0342-8726, Preibisch, Stephan ORCID: https://orcid.org/0000-0002-0276-494X, Camargo, Anamaria Aranha, Masotti, Cibele ORCID: https://orcid.org/0000-0003-4462-0941 and Costa, Erico Tosoni ORCID: https://orcid.org/0000-0001-7413-4675
Cancers 17
(23): 3851.
December 2025
Visualizing sarcomere and cellular dynamics in skeletal muscle to improve cell therapies.
Hüttemeister, J., Rudolph, F., Radke, M.H. ORCID: https://orcid.org/0000-0003-0112-9917, Fink, C., Friedrich, D. ORCID: https://orcid.org/0000-0003-2144-9280, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114, Wagner, E., Lehnart, S.E. ORCID: https://orcid.org/0000-0002-8115-3513 and Gotthardt, M. ORCID: https://orcid.org/0000-0003-1788-3172
eLife 13
: e95597.
17 December 2024
Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
BMC Biology 20
(1): 277.
13 December 2022
Best practice standards for circular RNA research.
Nielsen, A.F. ORCID: https://orcid.org/0000-0003-2653-4863, Bindereif, A., Bozzoni, I. ORCID: https://orcid.org/0000-0002-3485-8537, Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S. ORCID: https://orcid.org/0000-0002-5980-7939, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J. ORCID: https://orcid.org/0000-0003-1631-6440, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Suenkel, C. ORCID: https://orcid.org/0000-0002-5326-6043 and Kjems, J. ORCID: https://orcid.org/0000-0003-4128-9317
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. ORCID: https://orcid.org/0000-0001-7702-5749, Morao, A.K. ORCID: https://orcid.org/0000-0003-2194-8071, Kim, J. ORCID: https://orcid.org/0000-0001-9473-3093, Jimenez, D.S. ORCID: https://orcid.org/0000-0003-0943-9063, Maryn, N. ORCID: https://orcid.org/0000-0002-0975-3354, Bikkasani, K. ORCID: https://orcid.org/0000-0002-4000-1863, Carrozza, M.J., Albritton, S.E. ORCID: https://orcid.org/0000-0001-6093-9560, Kramer, M. ORCID: https://orcid.org/0000-0002-1643-0756, Street, L.A. ORCID: https://orcid.org/0000-0002-5473-6713, Cerimi, K. ORCID: https://orcid.org/0000-0003-0775-3032, Schumann, V.F. ORCID: https://orcid.org/0000-0003-0227-7428, Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Ercan, S. ORCID: https://orcid.org/0000-0001-7297-1648
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. ORCID: https://orcid.org/0000-0001-8231-2195, Dos Santos, N., Contzen, J., Stachelscheid, H., Costa, E.T., Mergenthaler, P. ORCID: https://orcid.org/0000-0002-9753-6711 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Bioinformatics 37
(18): 3088-3090.
15 September 2021
Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N. ORCID: https://orcid.org/0000-0002-1159-0689, Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Wisniewski, J., Yaniv, Z., Desai, R.A., Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
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. ORCID: https://orcid.org/0000-0002-5013-255X, Xin, Y. ORCID: https://orcid.org/0000-0003-3656-4310, Ling, L. ORCID: https://orcid.org/0000-0002-1754-6902, Mühling, B. ORCID: https://orcid.org/0000-0003-4901-0560, Jaenichen, R., Hörl, D. ORCID: https://orcid.org/0000-0003-1710-1708, Bunk, D. ORCID: https://orcid.org/0000-0001-9838-7626, Harz, H. ORCID: https://orcid.org/0000-0003-1218-2107, Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449, Wang, Y., Osipova, E., Museridze, M., Dharmadhikari, D., Murphy, E. ORCID: https://orcid.org/0000-0002-3771-7211, Rohs, R. ORCID: https://orcid.org/0000-0003-1752-1884, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Prud'homme, B. ORCID: https://orcid.org/0000-0003-2889-9081 and Gompel, N. ORCID: https://orcid.org/0000-0003-3358-7963
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. ORCID: https://orcid.org/0000-0003-3565-0698, Yu, L., Bergmann, N., Friedrich, D. ORCID: https://orcid.org/0000-0003-2144-9280, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Wagner, E., Lehnart, S.E. ORCID: https://orcid.org/0000-0002-8115-3513, Gregorio, C.C. and Gotthardt, M. ORCID: https://orcid.org/0000-0003-1788-3172
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. ORCID: https://orcid.org/0000-0003-2144-9280, Friedel, L., Finzel, A., Herrmann, A., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X and Loewer, A. ORCID: https://orcid.org/0000-0002-8819-3040
Molecular Systems Biology 15
(12): e9068.
1 December 2019
BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.
Hörl, D. ORCID: https://orcid.org/0000-0003-1710-1708, Rojas Rusak, F. ORCID: https://orcid.org/0000-0002-0637-9467, Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Tillberg, P. ORCID: https://orcid.org/0000-0002-2568-2365, Randel, N. ORCID: https://orcid.org/0000-0002-7817-4137, Chhetri, R.K. ORCID: https://orcid.org/0000-0001-6039-4505, Cardona, A. ORCID: https://orcid.org/0000-0001-6039-4505, Keller, P.J. ORCID: https://orcid.org/0000-0003-2896-4920, Harz, H., Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449, Treier, M. ORCID: https://orcid.org/0000-0002-8751-1246 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Nature Methods 16
(9): 870-874.
September 2019
Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I. ORCID: https://orcid.org/0000-0003-0640-4519, Bröhl, D., Zyrianova, T. ORCID: https://orcid.org/0000-0003-4295-6708, Isomura, A., Czajkowski, M.T. ORCID: https://orcid.org/0000-0002-0122-1943, Kapoor, V. ORCID: https://orcid.org/0000-0001-5331-7966, Griger, J. ORCID: https://orcid.org/0000-0001-8666-3371, Ruffault, P.L. ORCID: https://orcid.org/0000-0002-3378-3828, Mademtzoglou, D. ORCID: https://orcid.org/0000-0002-4494-7234, Zammit, P.S., Wunderlich, T., Spuler, S. ORCID: https://orcid.org/0000-0002-0155-1117, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Kageyama, R. and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
Genes & Development 33
(9-10): 524-535.
1 May 2019
MTrack: automated detection, tracking, and analysis of dynamic microtubules.
Kapoor, V. ORCID: https://orcid.org/0000-0001-5331-7966, Hirst, W.G., Hentschel, C., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-1159-0689, Wang, C., Höckendorf, B., Pujala, A., Tanimoto, M., Mu, Y. ORCID: https://orcid.org/0000-0001-9297-4854, Yang, C.T., Wittenbach, J.D., Freeman, J., Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Koyama, M., Keller, P.J. ORCID: https://orcid.org/0000-0003-2896-4920 and Ahrens, M.B. ORCID: https://orcid.org/0000-0002-3457-4462
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. ORCID: https://orcid.org/0000-0001-7702-5749, Blum, H., van Steensel, B. and Classen, A.K. ORCID: https://orcid.org/0000-0001-5157-0749
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. ORCID: https://orcid.org/0000-0002-5926-7338, Tinevez, J.Y., Pietzsch, T., Stamataki, E., Harich, B., Guignard, L. ORCID: https://orcid.org/0000-0002-3686-1385, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Shorte, S., Keller, P.J., Tomancak, P. ORCID: https://orcid.org/0000-0002-2222-9370 and Pavlopoulos, A. ORCID: https://orcid.org/0000-0002-0230-5815
eLife 7
: e34410.
29 March 2018
Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells.
Mönke, G. ORCID: https://orcid.org/0000-0002-3521-715X, Cristiano, E., Finzel, A., Friedrich, D. ORCID: https://orcid.org/0000-0003-2144-9280, Herzel, H., Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114 and Loewer, A. ORCID: https://orcid.org/0000-0002-8819-3040
Scientific Reports 7
: 46571.
18 April 2017
Autoionization in time-dependent density-functional theory.
Kapoor, V. ORCID: https://orcid.org/0000-0001-5331-7966
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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-0276-494X, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X and Tomancak, P. ORCID: https://orcid.org/0000-0002-2222-9370
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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X and Tomancak, P.
Methods 68
(1): 60-73.
15 June 2014
Efficient Bayesian-based multiview deconvolution.
Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-0276-494X, Corcoran, D.L., Jarrells, J., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, 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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X and Berger, H.
Methods in Molecular Biology 576
: 375-407.
2010
Globally optimal stitching of tiled 3D microscopic image acquisitions.
Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X
Algorithms for Molecular Biology 3
: 11.
29 August 2008
"Hook"-calibration of GeneChip-microarrays: theory and algorithm.
Binder, H. and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Algorithms for Molecular Biology 3
: 12.
29 August 2008
GeneChip microarrays-signal intensities, RNA concentrations and probe sequences.
Binder, H. and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-0276-494X
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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-2353-5310, Epstein, L. and Guignard, L. ORCID: https://orcid.org/0000-0002-3686-1385
In:
Cell Movement in Health and Disease.
Academic Press, London, 341-361.
ISBN 978-0-323-90195-6
2022
Adaptive optics.
Vladimirov, Nikita ORCID: https://orcid.org/0000-0002-1159-0689 and Tao, Xiaodong
In:
Imaging Modalities for Biological and Preclinical Research: A Compendium.
IPEM-IOP Series in Physics and Engineering in Medicine and Biology, Volume 1, Part I: Ex vivo biological imaging
.
IOP Publishing, Bristol, United Kingdom, I.2.e-1-I.2.e-11.
ISBN 978-0-7503-3057-2
May 2021
Review
Light sheet fluorescence microscopy.
Stelzer, E.H.K. ORCID: https://orcid.org/0000-0003-1545-0736, Strobl, F., Chang, B.J., Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, McDole, K. and Fiolka, R.
Nature Reviews Methods Primers 1
(1): 73.
3 November 2021
Light-microscopy methods in C. elegans research.
Breimann, L. ORCID: https://orcid.org/0000-0001-7702-5749, Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
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. ORCID: https://orcid.org/0000-0002-0276-494X 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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. ORCID: https://orcid.org/0000-0002-0276-494X, 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
Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos.
Breimann, L. ORCID: https://orcid.org/0000-0001-7702-5749, Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Zouinkhi, M. ORCID: https://orcid.org/0000-0002-9441-2908, Kolyvanov, K., Street, L.A. ORCID: https://orcid.org/0000-0002-5473-6713, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X and Ercan, S. ORCID: https://orcid.org/0000-0001-7297-1648
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. ORCID: https://orcid.org/0000-0003-0112-9917, Fink, C., Friedrich, D. ORCID: https://orcid.org/0000-0003-2144-9280, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114, Wagner, E., Lehnart, S.E. and Gotthardt, M. ORCID: https://orcid.org/0000-0003-1788-3172
bioRxiv
: 2024.02.01.578471.
7 February 2024
Dataset
Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.
Stumberger, Gabriela ORCID: https://orcid.org/0000-0002-5630-0032, Hörl, David ORCID: https://orcid.org/0000-0003-1710-1708, Tsouraki, Dimitra ORCID: https://orcid.org/0009-0006-1428-6718, Steinek, Clemens ORCID: https://orcid.org/0000-0003-3590-2103, Oudelaar, Aukje Marieke ORCID: https://orcid.org/0000-0002-4016-6158, Leonhardt, Heinrich ORCID: https://orcid.org/0000-0002-5086-6449 and Harz, Hartmann ORCID: https://orcid.org/0000-0003-1218-2107
[Dataset]
14 September 2025
This list was generated on Mon Jul 13 04:43:44 2026 UTC.
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