Xiongtao_Ruan.jpg

Xiongtao Ruan


[email protected]
Postdoctoral Research Fellow
Advanced Bioimaging Center
Department of Molecular and Cell Biology
University of California, Berkeley


I’m a postdoctoral research fellow in the Advanced Bioimaging Center at the University of California, Berkeley. I’m working with Drs. Gokul Upadhyayula and Eric Betzig. In May 2019, I obtained my Ph.D. in Computational Biology under the supervision of Dr. Robert F. Murphy at Carnegie Mellon University.

I’m interested in bioimage processing and analysis, image-based modeling, and computing-empowered microscopy. My goal is to advance computational methods for cutting-edge microscopy techniques to gain deeper insights into biological phenomena. Currently, I’m focusing on developing scalable and efficient image processing methods for petabyte-scale light sheet microscopy data in order to understand biological facts from seemingly incomprehensible large biological samples, such as the mouse brain, human brain, and more.

Education and employment


Selected publications

  1. Nanoscale volumetric fluorescence imaging via photochemical sectioning
    Wang, W.*,  Ruan, X.*, Liu, G.*, Milkie, DE., Li, W., Betzig, E., Upadhyayula, S., and Gao, R.
    bioRxiv, 2024
  2. Image processing tools for petabyte-scale light sheet microscopy data
    Ruan, X.#, Mueller, M., Liu, G., Görlitz, F., Fu, T., Milkie, DE., Lillvis, JL., Kuhn, A., Chong, JG., Hong, JL., Herr, CA., Hercule, W., Nienhaus, M., Killilea, AN., Betzig, E.#, and Upadhyayula, S.#
    Nature Methods, 2024
  3. Characterization, comparison, and optimization of lattice light sheets
    Liu, G.*,  Ruan, X.*, Milkie, DE., Görlitz, F., Mueller, M., Hercule, W., Killilea, A., Betzig, E., and Upadhyayula, S.
    Science Advances, 2023
  4. Evaluation of methods for generative modeling of cell and nuclear shape
    Ruan, X., and Murphy, RF.
    Bioinformatics, 2019
  5. Image-based spatiotemporal causality inference for protein signaling networks
    Ruan, X., Wülfing, C., and Murphy, RF.
    Bioinformatics, Jul 2017