Publications

2019

• Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish
  G. Shah, K. Thierbach, B. Schmid, J. Waschke, A. Reade, M. Hlawitschka, I. Roeder, N. Scherf, J. Huisken
  Nature Communications (in press)
• Image quality guided smart rotation improves coverage in microscopy
  J. He, J. Huisken
  Nature Communications (in press)
• Putting Advanced Microscopy in the Hands of Biologists
  R.M. Power, J. Huisken
  Nature Methods 16, 1069 (2019)
• A conserved regulatory program drives emergence of the lateral plate mesoderd
  K.D. Prummel, …, J. Huisken, M.H. Yun, L. Christiaen, Z. Kozmik, P. Müller, M. Bronner, R. Krumlauf, C. Mosimann
  Nature Communications, 10, 3857 (2019)
• Cerebrovascular endothelial cells form transient Notch-dependent cystic structures in zebrafish
  E. Kugler, M. v. Lessen, S. Daetwyler, K. Chhabria, A.M. Savage, V. Silva, K. Plant, R.M. McDonald, J. Huisken, R.N. Wilkinson, S. Schulte-Merker, P. Armitage, T.J. Chico
  EMBO Reports e47047 (2019)
• 3Dscript: Animating 3D/4D microscopy data using a natural language based syntax
  B. Schmid, P. Tripal, T. Fraaß, C. Kersten, B. Ruder, A. Grüneboom, J. Huisken, R. Palmisano
  Nature Methods 16, 278 (2019)
• Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
  S. Daetwyler, U. Günther, C.D. Modes, K. Harrington, J. Huisken
  Development 146, dev173757 (2019)
• Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
  N.D. Chrispijn, D.M. Elurbe, M. Mickoleit, …, J. Huisken, J. Bakkers, L.M. Kamminga
  Sci. Reports 9, 4327 (2019)

2018

• Dynamic, non-contact 3D sample rotation for microscopy
  F. Berndt, G. Shah, J. Brugues, J. Huisken
  Nature Communications 9, 5025 (2018)
• Neuromesodermal Progenitors are a Conserved Source of Spinal Cord with Divergent Growth Dynamics
  A. Attardi, T. Fulton, M. Florescu, G. Shah, L. Muresan, J. Huisken, A. van Oudenaarden, B. Steventon
  Development 145, dev166728 (2018)
• Adaptable, illumination patterning light sheet microscopy
  Rory M Power, Jan Huisken
  Nat Scientific Reports, 8, 9615 (2018), doi:10.1038/s41598-018-28036-2
• Continuous addition of progenitors forms the cardiac ventricle in zebrafish
  Anastasia Felker, Karin D Prummel, Anne M Merks, Michaela Mickoleit, Eline C Brombacher, Jan Huisken, Daniela Panáková, Christian Mosimann
  Nat Communications, 9 2001 (2018), doi:10.1038/s41467-018-04402-6

2017

• Cell-accurate optical mapping across the entire developing heart
  Michael Weber, Nico Scherf, Alexander M Meyer, Daniela Panáková, Peter Kohl, Jan Huisken
  eLife 6 (2017), doi:10.7554/eLife.28307
• Intraoperative histology: Lightning 3D histopathology
  Rory M Power, Jan Huisken
  Nat Biomedical Engineering, 1 0101 (2017), doi:10.1038/s41551-017-0101
• A guide to light-sheet fluorescence microscopy for multiscale imaging
  Rory M Power, Jan Huisken
  Nat Methods, 14(4) 360-373 (2017), doi:10.1038/nmeth.4224
• Spectrally resolved, three-dimensional widefield microscopy
  Wiebke Jahr
  Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2017)
• Systematic Analysis of Vascular Patterning in Zebrafish
  Stephan Daetwyler
  Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2017)
• Spatiotemporal Deformable Prototypes for Motion Anomaly Detection
  Robert Bensch, Nico Scherf, Jan Huisken, Thomas Brox, Olaf Ronneberger
  Int J Comput Vis, 122 502-523 (2017), doi:10.1007/s11263-016-0934-1

2016

• Software Framework for Controlling Unsupervised Scientific Instruments
  Benjamin Schmid, Wiebke Jahr, Michael Weber, Jan Huisken
  PLoS ONE, 11(8) Art. No. e0161671 (2016), doi.org/10.1371/journal.pone.0161671
• Fast Fluorescence Microscopy with Light Sheets
  Stephan Daetwyler, Jan Huisken
  Biol. Bull., 231(1) 14-25 (2016), DOI: 10.1086/689588
• Imaging and Reconstructing the beating Heart and its Morphogenesis
  Michaela Mickoleit
  Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2016)
• Pan-embryo Cell Dynamics – Multidimensional imaging uncovers the blueprint of zebrafish development
  Gopi Shah
  Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2016)
• Biology-inspired visualization of morphogenetic motion in the zebrafish endoderm
  Konstantin Thierbach, Gopi Shah, Ingmar Glauche, Jan Huisken, Ingo Roeder, Nico Scherf
  In: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI) (2016), Piscataway, N.J., IEEE (2016), 925-929
• eduSPIM: Light Sheet Microscopy in the Museum
  Wiebke Jahr, Benjamin Schmid, Michael Weber, Jan Huisken
  PLoS ONE, 11(8) Art. No. e0161402 (2016), doi.org/10.1371/journal.pone.0161402

2015

• In vivo imaging of cardiac development and function in zebrafish using light sheet microscopy
  Michael Weber, Jan Huisken
  Swiss Med Wkly, 145 Art. No. w14227 (2015), DOI: 10.4414/smw.2015.14227
• Mechanical Coupling between Endoderm Invagination and Axis Extension in Drosophila
  Claire Lye, Guy Blanchard, Huw Naylor, Leila Muresan, Jan Huisken, Richard J Adams, Benedicte Sanson
  PLoS Biol, 13(11) Art. No. e1002292 (2015), doi.org/10.1371/journal.pbio.1002292
• Real-time multi-view deconvolution
  Benjamin Schmid, Jan Huisken
  Bioinformatics, 31(20) 3398-3400 (2015), https://doi.org/10.1093/bioinformatics/btv387
• Hyperspectral light sheet microscopy
  Wiebke Jahr, Benjamin Schmid, Christopher Schmied, Florian Fahrbach, Jan Huisken
  Nat Commun, 6 Art. No. 7990 (2015), doi:10.1038/ncomms899
• The smart and gentle microscope
  Nico Scherf, Jan Huisken
  Nat Biotechnol, 33(8) 815-818 (2015), doi:10.1038/nbt.3310
• All-optical 4D in vivo monitoring and manipulation of zebrafish cardiac conduction
  Michael Weber
  Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2015)
• Endothelial Cell Self-fusion during Vascular Pruning
  Anna Lenard, Stephan Daetwyler, Charles Betz, Elin Ellertsdottir, Heinz-Georg Belting, Jan Huisken, Markus Affolter
  PLoS Biol, 13(4) Art. No. e1002126 (2015, https://doi.org/10.1371/journal.pbio.1002126
• Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development
  Andrea Bassi, Benjamin Schmid, Jan Huisken
  Development, 142(5) 1016-1020 (2015), doi: 10.1242/dev.116970
• Regulation of β1 Integrin-Klf2-Mediated Angiogenesis by CCM Proteins
  Marc Renz, Cécile Otten, Eva Faurobert, Franziska Rudolph, Yu Zhu, Gwénola Boulday, Johan Duchene, Michaela Mickoleit, Ann-Christin Dietrich, Caroline Ramspacher, Emily Steed, Sandra Manet-Dupé, Alexander Benz, David Hassel, Julien Vermot, Jan Huisken, Elisabeth Tournier-Lasserve, Ute Felbor, Ulrich Sure, Corinne Albiges-Rizo, Salim Abdelilah-Seyfried
  Dev Cell, 32(2) 181-190 (2015), https://doi.org/10.1016/j.devcel.2014.12.016
• Guide to light-sheet microscopy for adventurous biologists
  Emmanuel G. Reynaud, Jan Peychl, Jan Huisken, Pavel Tomancak
  Nat Methods, 12(1) 30-34 (2015), doi:10.1038/nmeth.3222

2014

• Genome-wide RNA Tomography in the Zebrafish Embryo
  Jan Philipp Junker, Emily S. Noël, Victor Guryev, Kevin A Peterson, Gopi Shah, Jan Huisken, Andrew P. McMahon, Eugene Berezikov, Jeroen Bakkers, Alexander van Oudenaarden
  Cell, 159(3) 662-675 (2014), DOI: http://dx.doi.org/10.1016/j.cell.2014.09.038
• High-resolution reconstruction of the beating zebrafish heart
  Michaela Mickoleit, Benjamin Schmid, Michael Weber, Florian Fahrbach, Sonja Hombach, Sven Reischauer, Jan Huisken
  Nat Methods, 11(9) 919-922 (2014) , doi:10.1038/nmeth.3037
• Multilayer mounting for long-term light sheet microscopy of zebrafish
  Michael Weber, Michaela Mickoleit, Jan Huisken
  J Vis Exp, (84) Art. No. e51119 (2014), doi:10.3791/51119




• Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling
  Ashley L Alvers, Sean Ryan, Paul J Scherz, Jan Huisken, Michel Bagnat
  Development, 141(5) 1110-1119 (2014) , doi: 10.1242/dev.100313
• Light sheet microscopy
  Michael Weber, Michaela Mickoleit, Jan Huisken
  Methods Cell Biol, 123 193-215 (2014), https://doi.org/10.1016/B978-0-12-420138-5.00011-2

2013

• Rapid 3D light-sheet microscopy with a tunable lens
  Florian Fahrbach, Fabian F Voigt, Benjamin Schmid, Fritjof Helmchen, Jan Huisken
  Opt express, 21(18) 21010-21026 (2013), https://doi.org/10.1364/OE.21.021010
• High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics
  Benjamin Schmid, Gopi Shah, Nico Scherf, Michael Weber, Konstantin Thierbach, Claudia Campos, Ingo Roeder, Pia Aanstad, Jan Huisken
  Nat Commun, 4 Art. No. 2207 (2013), doi:10.1038/ncomms3207
• OpenSPIM: an open access light sheet microscopy platform
  Peter Gabriel Pitrone, Johannes Schindelin, Luke Stuyvenberg, Stephan Preibisch, Michael Weber, Kevin W Eliceiri, Jan Huisken, Pavel Tomancak
  Nat Methods, 10(7) 598-599 (2013), doi:10.1038/nmeth.2507

2012

• Transgenic zebrafish illuminate the dynamics of thyroid morphogenesis and its relationship to cardiovascular development
  Robert Opitz, Emilie Maquet, Jan Huisken, Francesco Antonica, Achim Trubiroha, Gaëlle Pottier, Veerle Janssens, Sabine Costagliola
  Dev Biol, 372(2) 203-216 (2012), https://doi.org/10.1016/j.ydbio.2012.09.011
• Fibrillin-2b regulates endocardial morphogenesis in zebrafish
  Katharine Mellman, Jan Huisken, Colin Dinsmore, Cornelia Hoppe, Didier Y.R. Stainier
  Dev Biol, 372(1) 111-119 (2012), https://doi.org/10.1016/j.ydbio.2012.07.015
• Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope
  Anna Kaufmann, Michaela Mickoleit, Michael Weber, Jan Huisken
  Development, 139(17) 3242-3247 (2012), doi: 10.1242/dev.082586
• Omnidirectional microscopy
  Michael Weber, Jan Huisken
  Nat Methods, 9(7) 656-657 (2012), doi:10.1038/nmeth.2022
• Fiji: an open-source platform for biological-image analysis
  Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Dan White, Volker Hartenstein, Kevin W Eliceiri, Pavel Tomancak, Albert Cardona
  Nat Methods, 9(7) 676-682 (2012), doi:10.1038/nmeth.2019
• The Popeye domain containing 2 (popdc2) gene in zebrafish is required for heart and skeletal muscle development
  Bettina C Kirchmaier, Kar Lai Poon, Thorsten Schwerte, Jan Huisken, Christoph Winkler, Benno Jungblut, Didier Y.R. Stainier, Thomas Brand
  Dev Biol, 363(2) 438-450 (2012), https://doi.org/10.1016/j.ydbio.2012.01.015
• Slicing embryos gently with laser light sheets
  Jan Huisken
  Bioessays, 34(5) 406-411 (2012), DOI: 10.1002/bies.201100120

2011

• A new ImageJ plug-in “ActogramJ” for chronobiological analyses
  Benjamin Schmid, Charlotte Helfrich-Förster, Taishi Yoshii
  J Biol Rhythms, 26(5) 464-467 (2011), https://doi.org/10.1177/0748730411414264
• Light sheet microscopy for real-time developmental biology
  Michael Weber, Jan Huisken
  Curr Opin Genet Dev, 21(5) 566-572 (2011), https://doi.org/10.1016/j.gde.2011.09.009
• Under-filling trapping objectives optimizes the use of the available laser power in optical tweezers
  Mohammed Mahamdeh, Citlali Perez Campos, Erik Schäffer
  Opt express, 19(12) 11759-11768 (2011), https://doi.org/10.1364/OE.19.011759

2010

• Optogenetic control of cardiac function
  Aristides B. Arrenberg, Didier Y.R. Stainier, Herwig Baier, Jan Huisken
  Science, 330(6006) 971-974 (2010), DOI: 10.1126/science.1195929
• A dual role for ErbB2 signaling in cardiac trabeculation
  Jiandong Liu, Michael Bressan, David Hassel, Jan Huisken, David Staudt, Kazu Kikuchi, Kenneth D Poss, Takashi Mikawa, Didier Y.R. Stainier
  Development, 137(22) 3867-3875 (2010), doi: 10.1242/dev.053736
• Cse1l Is a Negative Regulator of CFTR-Dependent Fluid Secretion
  Michel Bagnat, Adam Navis, Sara Herbstreith, Koroboshka Brand-Arzamendi, Silvia Curado, Sherif Gabriel, Keith Mostov, Jan Huisken, Didier Y.R. Stainier
  Curr Biol, 20(20) 1840-1845 (2010), doi: 10.1016/j.cub.2010.09.012

2009

• Arterial-venous segregation by selective cell sprouting: an alternative mode of blood vessel formation
  Shane P Herbert, Jan Huisken, Tyson N Kim, Morri E Feldman, Benjamin T Houseman, Rong A Wang, Kevan M Shokat, Didier Y.R. Stainier
  Science, 326(5950) 294-298 (2009), doi: 10.1126/science.1178577
• The extracellular domain of Smoothened regulates ciliary localization and is required for high-level Hh signaling
  Pia Aanstad, Nicole Santos, Kevin C Corbit, Paul J Scherz, Le A Trinh, Willi Salvenmoser, Jan Huisken, Jeremy F Reiter, Didier Y.R. Stainier
  Curr Biol, 19(12) 1034-1039 (2009) , doi: 10.1016/j.cub.2009.04.053
• Selective plane illumination microscopy techniques in developmental biology
  Jan Huisken, Didier Y.R. Stainier
  Development, 136(12) 1963-1975 (2009), doi: 10.1242/dev.022426
• Genetic evidence for a noncanonical function of seryl-tRNA synthetase in vascular development
  Wiebke Herzog, Katja Müller, Jan Huisken, Didier Y.R. Stainier
  Circ Res, 104(11) 1260-1266 (2009), doi: 10.1161/CIRCRESAHA.108.191718

2008

• Regulation of neurocoel morphogenesis by Pard6 gamma b
  Chantilly Munson, Jan Huisken, Nana Bit-Avragim, Taiyi Kuo, P D Dong, Elke A Ober, Heather Verkade, Salim Abdelilah-Seyfried, Didier Y.R. Stainier
  Dev Biol, 324(1) 41-54 (2008), https://doi.org/10.1016/j.ydbio.2008.08.033
• Multiple roles for Med12 in vertebrate endoderm development
  Chong Hyun Shin, Won-Suk Chung, Sung-Kook Hong, Elke A Ober, Heather Verkade, Holly A Field, Jan Huisken, Didier Y.R. Stainier
  Dev Biol, 317(2) 467-479 (2008), doi: 10.1016/j.ydbio.2008.02.031
• Genetic and physiologic dissection of the vertebrate cardiac conduction system
  Neil C Chi, Robin M Shaw, Benno Jungblut, Jan Huisken, Tania Ferrer, Rima Arnaout, Ian Scott, Dimitris Beis, Tong Xiao, Herwig Baier, Lily Y Jan, Martin Tristani-Firouzi, Didier Y.R. Stainier
  PLoS Biol, 6(5) 109-109 (2008), https://doi.org/10.1371/journal.pbio.0060109
• High-speed imaging of developing heart valves reveals interplay of morphogenesis and function
  Paul J Scherz, Jan Huisken, Pankaj Sahai-Hernandez, Didier Y.R. Stainier
  Development, 135(6) 1179-1187 (2008), doi: 10.1242/dev.010694

2007

• Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM)
  Jan Huisken, Didier Y.R. Stainier
  Opt Lett, 32(17) 2608-2610 (2007), https://doi.org/10.1364/OL.32.002608
• Zebrafish model for human long QT syndrome
  Rima Arnaout, Tania Ferrer, Jan Huisken, Kenneth Spitzer, Didier Y.R. Stainier, Martin Tristani-Firouzi, Neil C Chi
  Proc Natl Acad Sci U.S.A., 104(27) 11316-11321 (2007), doi: 10.1073/pnas.0702724104
• Multi-view image fusion improves resolution in three-dimensional microscopy
  Jim Swoger, Peter Verveer, Klaus Greger, Jan Huisken, Ernst H K Stelzer
  Opt express, 15(13) 8029-8042 (2007), https://doi.org/10.1364/OE.15.008029
• Three-dimensional optical manipulation using four collimated intersecting laser beams
  Jan Huisken, Jim Swoger, Ernst H K Stelzer
  Opt express, 15(8) 4921-4928 (2007), https://doi.org/10.1364/OE.15.004921

2004

• Optical sectioning deep inside live embryos by selective plane illumination microscopy
  Jan Huisken, Jim Swoger, Filippo Del Bene, Jochen Wittbrodt, Ernst H K Stelzer
  Science, 305(5686) 1007-1009 (2004), DOI: 10.1126/science.1100035

2003

• Multiple imaging axis microscopy improves resolution for thick-sample applications
  Jim Swoger, Jan Huisken, Ernst H K Stelzer
  Opt Lett, 28(18) 1654-1656 (2003), https://doi.org/10.1364/OL.28.001654

2002

• Optical scanning holography as a technique for high-resolution three-dimensional biological microscopy
  Jim Swoger, Manuel Martínez-Corral, Jan Huisken, Ernst H K Stelzer
  J Opt Soc Am A Opt Image Sci Vis, 19(9) 1910-1918 (2002), https://doi.org/10.1364/JOSAA.19.001910
• Optical levitation of absorbing particles with a nominally Gaussian laser beam
  Jan Huisken, Ernst H K Stelzer
  Opt Lett, 27(14) 1223-1225 (2002), https://doi.org/10.1364/OL.27.001223