Jan Huisken

Director, Morgridge Medical Engineering and Professor, Biomedical Engineering


Medical Engineering


(608) 316-4417


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The overall goal of my lab is the systematic study of developmental processes in living organisms by noninvasive biomedical imaging techniques such as optical microscopy. Of primary interest is the investigation of organogenesis in zebrafish with special emphasis on the function and morphogenesis of the cardiovascular system and the endoderm. We develop novel quantitative microscopy tools and experimental strategies to understand and describe tissue dynamics on a cellular level. High-speed fluorescence microscopy is the primary tool to capture the dynamics of a heartbeat and the fate of single cells during organogenesis.

In our interdisciplinary lab we address all experimental steps from innovative transgenic lines and microscope development to systematic image processing. The biologists in the lab have the opportunity to use cutting edge microscopy to perform experiments that are impossible with off-the-shelf instruments. At the same time the physicists in the lab can build novel microscopes that are immediately applied to address exciting biological questions.

Areas of Expertise

  • Selective plane illumination microscopy (SPIM)
  • High-speed fluorescence microscopy
  • Organogenesis
  • Zebrafish, with special focus on the cardiovascular system and endoderm


Since 2010

Research Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics


Postdoctoral work at the University of California, San Francisco


Postdoctoral work at the EMBL-Heidelberg


PhD work at the EMBL-Heidelberg, PhD in Physics, University of Freiburg

Selected Publications


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