Publications

Journal Articles

  1. Y. Liu, K. Weiss, N. Navab, C. Marr, J. Huisken, T. Peng, “DeStripe: a Self2Self Spatio-Spectral graph neural network with unfolded hessian for stripe artifact removal in light-sheet microscopy”, (2022).
  2. A. Michaud, M. Leda, Z. T. Swider, S. Kim, J. He, J. Landino, J. R. Valley, J. Huisken, A. B. Goryachev, G. Dassow, W. M. Bement, “A versatile cortical pattern-forming circuit based on rho, f-actin, ect2, and RGA-3/4”, J. Cell Biol. 221, 10.1083/jcb.202203017 (2022).
  3. J. Fadul, T. Zulueta-Coarasa, G. M. Slattum, N. M. Redd, M. F. Jin, M. J. Redd, S. Daetwyler, D. Hedeen, J. Huisken, J. Rosenblatt, “KRas-transformed epithelia cells invade and partially dedifferentiate by basal cell extrusion”, Nat. Commun. 12, 7180 (2021).
  4. A. J. Ropelewski, M. A. Rizzo, J. R. Swedlow, J. Huisken, P. Osten, N. Khanjani, K. Weiss, V. Bakalov, M. Engle, L. Gridley, M. Krzyzanowski, T. Madden, D. Maiese, J. Waterfield, D. Williams, C. Hamilton, W. Huggins, “Essential metadata for 3D BRAIN microscopy”, (2021).
  5. A. Schlaeppi, A. Graves, M. Weber, J. Huisken, “Light sheet microscopy of fast cardiac dynamics in zebrafish embryos”, J. Vis. Exp., 10.3791/62741 (2021).
  6. M. E. Skibba, X. Xu, K. Weiss, J. Huisken, A. R. Brasier, “Role of secretoglobin+ (club cell) NFκB/RelA-TGFβ signaling in aero-allergen-induced epithelial plasticity and subepithelial myofibroblast transdifferentiation”, Respir. Res. 22, 315 (2021).
  7. J. Waschke, M. Hlawitschka, K. Anlas, V. Trivedi, I. Roeder, J. Huisken, N. Scherf, “Linus: conveniently explore, share, and present large-scale biological trajectory data in a web browser”, PLoS Comput. Biol. 17, e1009503 (2021).
  8. M. Weber, J. Huisken, “Multidisciplinarity is critical to unlock the full potential of modern light microscopy”, Front Cell Dev Biol 9, 739015 (2021).
  9. K. R. Weiss, F. F. Voigt, D. P. Shepherd, J. Huisken, “Tutorial: practical considerations for tissue clearing and imaging”, Nat. Protoc. 16, 2732–2748 (2021).
  10. C. Zhao, J. J. Lancman, Y. Yang, K. P. Gates, D. Cao, L. Barske, J. Matalonga, X. Pan, J. He, A. Graves, J. Huisken, C. Chen, P. D. S. Dong, “Intrahepatic cholangiocyte regeneration from an fgf-dependent extrahepatic progenitor niche in a zebrafish model of alagille syndrome”, Hepatology, 10.1002/hep.32173 (2021).
  11. N. Asokan, S. Daetwyler, S. N. Bernas, C. Schmied, S. Vogler, K. Lambert, M. Wobus, M. Wermke, G. Kempermann, J. Huisken, M. Brand, M. Bornhäuser, “Long-term in vivo imaging reveals tumor-specific dissemination and captures host tumor interaction in zebrafish xenografts”, Sci. Rep. 10, 13254 (2020).
  12. K. Chhabria, K. Plant, O. Bandmann, R. N. Wilkinson, C. Martin, E. Kugler, P. A. Armitage, P. L. Santoscoy, V. T. Cunliffe, J. Huisken, A. McGown, T. Ramesh, T. J. Chico, C. Howarth, “The effect of hyperglycemia on neurovascular coupling and cerebrovascular patterning in zebrafish”, J. Cereb. Blood Flow Metab. 40, 298–313 (2020).
  13. P. F. Favreau, J. He, D. A. Gil, D. A. Deming, J. Huisken, M. C. Skala, “Label-free redox imaging of patient-derived organoids using selective plane illumination microscopy”, Biomed. Opt. Express 11, 2591–2606 (2020).
  14. J. He, J. Huisken, “Image quality guided smart rotation improves coverage in microscopy”, Nat. Commun. 11, 150 (2020).
  15. E. E. Rosowski, J. He, J. Huisken, N. P. Keller, A. Huttenlocher, “Efficacy of voriconazole against aspergillus fumigatus infection depends on host immune function”, Antimicrob. Agents Chemother. 64, 10.1128/AAC.00917-19 (2020).
  16. N. D. Chrispijn, D. M. Elurbe, M. Mickoleit, M. Aben, D. E. M. Bakker, K. M. Andralojc, J. Huisken, J. Bakkers, L. M. Kamminga, “Loss of the polycomb group protein rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development”, Sci. Rep. 9, 4327 (2019).
  17. S. Daetwyler, U. Günther, C. D. Modes, K. Harrington, J. Huisken, “Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish”, Development 146, 10.1242/dev.173757 (2019).
  18. E. C. Kugler, M. Lessen, S. Daetwyler, K. Chhabria, A. M. Savage, V. Silva, K. Plant, R. B. MacDonald, J. Huisken, R. N. Wilkinson, S. Schulte-Merker, P. Armitage, T. J. Chico, “Cerebrovascular endothelial cells form transient notch-dependent cystic structures in zebrafish”, EMBO Rep. 20, e47047 (2019).
  19. R. M. Power, J. Huisken, “Putting advanced microscopy in the hands of biologists”, Nat. Methods 16, 1069–1073 (2019).
  20. K. D. Prummel, C. Hess, S. Nieuwenhuize, H. J. Parker, K. W. Rogers, I. Kozmikova, C. Racioppi, E. C. Brombacher, A. Czarkwiani, D. Knapp, S. Burger, E. Chiavacci, G. Shah, A. Burger, J. Huisken, M. H. Yun, L. Christiaen, Z. Kozmik, P. Müller, M. Bronner, R. Krumlauf, C. Mosimann, “A conserved regulatory program initiates lateral plate mesoderm emergence across chordates”, Nat. Commun. 10, 3857 (2019).
  21. B. Schmid, P. Tripal, T. Fraa, C. Kersten, B. Ruder, A. Grüneboom, J. Huisken, R. Palmisano, “3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax”, Nat. Methods 16, 278–280 (2019).
  22. G. Shah, K. Thierbach, B. Schmid, J. Waschke, A. Reade, M. Hlawitschka, I. Roeder, N. Scherf, J. Huisken, “Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish”, Nat. Commun. 10, 5753 (2019).
  23. A. Attardi, T. Fulton, M. Florescu, G. Shah, L. Muresan, M. O. Lenz, C. Lancaster, J. Huisken, A. Oudenaarden, B. Steventon, “Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics”, Development 145, dev.166728 (2018).
  24. F. Berndt, G. Shah, R. M. Power, J. Brugués, J. Huisken, “Dynamic and non-contact 3D sample rotation for microscopy”, Nat. Commun. 9, 5025 (2018).
  25. A. Felker, K. D. Prummel, A. M. Merks, M. Mickoleit, E. C. Brombacher, J. Huisken, D. Panáková, C. Mosimann, “Continuous addition of progenitors forms the cardiac ventricle in zebrafish”, Nat. Commun. 9, 2001 (2018).
  26. R. M. Power, J. Huisken, “Adaptable, illumination patterning light sheet microscopy”, Sci. Rep. 8, 9615 (2018).
  27. R. Bensch, N. Scherf, J. Huisken, T. Brox, O. Ronneberger, “Spatiotemporal deformable prototypes for motion anomaly detection”, Int. J. Comput. Vis. 122, 502–523 (2017).
  28. R. M. Power, J. Huisken, “A guide to light-sheet fluorescence microscopy for multiscale imaging”, Nat. Methods 14, 360–373 (2017).
  29. R. M. Power, J. Huisken, “Intraoperative histology: lightning 3D histopathology”, Nature Biomedical Engineering 1, 1–2 (2017).
  30. M. Weber, N. Scherf, A. M. Meyer, D. Panáková, P. Kohl, J. Huisken, “Cell-accurate optical mapping across the entire developing heart”, Elife 6, e28307 (2017).
  31. S. Daetwyler, J. Huisken, “Fast fluorescence microscopy with light sheets”, Biol. Bull. 231, 14–25 (2016).
  32. W. Jahr, B. Schmid, M. Weber, J. Huisken, “eduSPIM: light sheet microscopy in the museum”, PLoS One 11, e0161402 (2016).
  33. B. Schmid, W. Jahr, M. Weber, J. Huisken, “Software framework for controlling unsupervised scientific instruments”, PLoS One 11, e0161671 (2016).
  34. A. Bassi, B. Schmid, J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development”, Development 142, 1016–1020 (2015).
  35. W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, J. Huisken, “Hyperspectral light sheet microscopy”, Nat. Commun. 6, 7990 (2015).
  36. A. Lenard, S. Daetwyler, C. Betz, E. Ellertsdottir, H.-G. Belting, J. Huisken, M. Affolter, “Endothelial cell self-fusion during vascular pruning”, PLoS Biol. 13, e1002126 (2015).
  37. C. M. Lye, G. B. Blanchard, H. W. Naylor, L. Muresan, J. Huisken, R. J. Adams, B. Sanson, “Mechanical coupling between endoderm invagination and axis extension in drosophila”, PLoS Biol. 13, e1002292 (2015).
  38. M. Renz, C. Otten, E. Faurobert, F. Rudolph, Y. Zhu, G. Boulday, J. Duchene, M. Mickoleit, A.-C. Dietrich, C. Ramspacher, E. Steed, S. Manet-Dupé, A. Benz, D. Hassel, J. Vermot, J. Huisken, E. Tournier-Lasserve, U. Felbor, U. Sure, C. Albiges-Rizo, S. Abdelilah-Seyfried, “Regulation of β1 integrin-klf2-mediated angiogenesis by CCM proteins”, Dev. Cell 32, 181–190 (2015).
  39. E. G. Reynaud, J. Peychl, J. Huisken, P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists”, Nat. Methods 12, 30–34 (2015).
  40. N. Scherf, J. Huisken, “The smart and gentle microscope”, Nat. Biotechnol. 33, 815–818 (2015).
  41. B. Schmid, J. Huisken, “Real-time multi-view deconvolution”, Bioinformatics 31, 3398–3400 (2015).
  42. M. Weber, J. Huisken, “In vivo imaging of cardiac development and function in zebrafish using light sheet microscopy”, Swiss Med. Wkly 145, w14227 (2015).
  43. A. L. Alvers, S. Ryan, P. J. Scherz, J. Huisken, M. Bagnat, “Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling”, Development 141, 1110–1119 (2014).
  44. J. P. Junker, E. S. Noël, V. Guryev, K. A. Peterson, G. Shah, J. Huisken, A. P. McMahon, E. Berezikov, J. Bakkers, A. Oudenaarden, “Genome-wide RNA tomography in the zebrafish embryo”, Cell 159, 662–675 (2014).
  45. M. Mickoleit, B. Schmid, M. Weber, F. O. Fahrbach, S. Hombach, S. Reischauer, J. Huisken, “High-resolution reconstruction of the beating zebrafish heart”, Nat. Methods 11, 919–922 (2014).
  46. M. Weber, M. Mickoleit, J. Huisken, “Multilayer mounting for long-term light sheet microscopy of zebrafish”, J. Vis. Exp., e51119 (2014).
  47. F. O. Fahrbach, F. F. Voigt, B. Schmid, F. Helmchen, J. Huisken, “Rapid 3D light-sheet microscopy with a tunable lens”, Opt. Express 21, 21010–21026 (2013).
  48. P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform”, Nat. Methods 10, 598–599 (2013).
  49. B. Schmid, G. Shah, N. Scherf, M. Weber, K. Thierbach, C. P. Campos, I. Roeder, P. Aanstad, J. Huisken, “High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics”, Nat. Commun. 4, 2207 (2013).
  50. O. Selchow, J. Huisken, “Lichtblattmikroskopie: Das Beleuchtungskonzept revolutioniert die 3D-Analyse lebender Proben”, Biophotonik 1, 24–27 (2013).
  51. J. Huisken, “Slicing embryos gently with laser light sheets”, Bioessays 34, 406–411 (2012).
  52. A. Kaufmann, M. Mickoleit, M. Weber, J. Huisken, “Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope”, Development 139, 3242–3247 (2012).
  53. B. C. Kirchmaier, K. L. Poon, T. Schwerte, J. Huisken, C. Winkler, B. Jungblut, D. Y. Stainier, T. Brand, “The popeye domain containing 2 (popdc2) gene in zebrafish is required for heart and skeletal muscle development”, Dev. Biol. 363, 438–450 (2012).
  54. K. Mellman, J. Huisken, C. Dinsmore, C. Hoppe, D. Y. Stainier, “Fibrillin-2b regulates endocardial morphogenesis in zebrafish”, Dev. Biol. 372, 111–119 (2012).
  55. R. Opitz, E. Maquet, J. Huisken, F. Antonica, A. Trubiroha, G. Pottier, V. Janssens, S. Costagliola, “Transgenic zebrafish illuminate the dynamics of thyroid morphogenesis and its relationship to cardiovascular development”, Dev. Biol. 372, 203–216 (2012).
  56. M. Weber, J. Huisken, “Omnidirectional microscopy”, Nat. Methods 9, 656–657 (2012).
  57. M. Weber, J. Huisken, “Light sheet microscopy for real-time developmental biology”, Curr. Opin. Genet. Dev. 21, 566–572 (2011).
  58. A. B. Arrenberg, D. Y. R. Stainier, H. Baier, J. Huisken, “Optogenetic control of cardiac function”, Science 330, 971–974 (2010).
  59. M. Bagnat, A. Navis, S. Herbstreith, K. Brand-Arzamendi, S. Curado, S. Gabriel, K. Mostov, J. Huisken, D. Y. R. Stainier, “Cse1l is a negative regulator of CFTR-dependent fluid secretion”, Curr. Biol. 20, 1840–1845 (2010).
  60. J. Liu, M. Bressan, D. Hassel, J. Huisken, D. Staudt, K. Kikuchi, K. D. Poss, T. Mikawa, D. Y. R. Stainier, “A dual role for ErbB2 signaling in cardiac trabeculation”, Development 137, 3867–3875 (2010).
  61. S. P. Herbert, J. Huisken, T. N. Kim, M. E. Feldman, B. T. Houseman, R. A. Wang, K. M. Shokat, D. Y. R. Stainier, “Arterial-venous segregation by selective cell sprouting: an alternative mode of blood vessel formation”, Science 326, 294–298 (2009).
  62. W. Herzog, K. Müller, J. Huisken, D. Y. R. Stainier, “Genetic evidence for a noncanonical function of seryl-tRNA synthetase in vascular development”, Circ. Res. 104, 1260–1266 (2009).
  63. J. Huisken, D. Y. R. Stainier, “Selective plane illumination microscopy techniques in developmental biology”, Development 136, 1963–1975 (2009).
  64. N. C. Chi, R. M. Shaw, B. Jungblut, J. Huisken, T. Ferrer, R. Arnaout, I. Scott, D. Beis, T. Xiao, H. Baier, L. Y. Jan, M. Tristani-Firouzi, D. Y. R. Stainier, “Genetic and physiologic dissection of the vertebrate cardiac conduction system”, PLoS Biol. 6, e109 (2008).
  65. C. Munson, J. Huisken, N. Bit-Avragim, T. Kuo, P. D. Dong, E. A. Ober, H. Verkade, S. Abdelilah-Seyfried, D. Y. R. Stainier, “Regulation of neurocoel morphogenesis by pard6 gamma b”, Dev. Biol. 324, 41–54 (2008).
  66. P. J. Scherz, J. Huisken, P. Sahai-Hernandez, D. Y. R. Stainier, “High-speed imaging of developing heart valves reveals interplay of morphogenesis and function”, Development 135, 1179–1187 (2008).
  67. R. Arnaout, T. Ferrer, J. Huisken, K. Spitzer, D. Y. R. Stainier, M. Tristani-Firouzi, N. C. Chi, “Zebrafish model for human long QT syndrome”, Proc. Natl. Acad. Sci. U. S. A. 104, 11316–11321 (2007).
  68. J. Huisken, J. Swoger, E. H. Stelzer, “Three-dimensional optical manipulation using four collimated intersecting laser beams”, Opt. Express 15, 4921–4928 (2007).
  69. J. Huisken, D. Y. R. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM)”, Opt. Lett. 32, 2608–2610 (2007).
  70. J. Swoger, P. Verveer, K. Greger, J. Huisken, E. H. K. Stelzer, “Multi-view image fusion improves resolution in three-dimensional microscopy”, Opt. Express 15, 8029–8042 (2007).
  71. J. Huisken, “Studying live embryos in 4d: selective plane illumination microscopy: a new technique for high-resolution four-dimensional imaging”, Biochem. 27, 13–16 (2005).
  72. J. Huisken, E. Stelzer, J. Swoger, “Selective plane illumination microscopy: optical sections from many directions”, GIT laboratory journal Europe 9, 27–29 (2005).
  73. J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy”, Science 305, 1007–1009 (2004).
  74. J. Swoger, J. Huisken, E. H. K. Stelzer, “Multiple imaging axis microscopy improves resolution for thick-sample applications”, Opt. Lett. 28, 1654–1656 (2003).
  75. J. Huisken, E. H. K. Stelzer, “Optical levitation of absorbing particles with a nominally gaussian laser beam”, Opt. Lett. 27, 1223–1225 (2002).
  76. J. Swoger, M. Martnez-Corral, J. Huisken, E. H. K. Stelzer, “Optical scanning holography as a technique for high-resolution three-dimensional biological microscopy”, J. Opt. Soc. Am. A Opt. Image Sci. Vis. 19, 1910–1918 (2002).