Xiongtao_Ruan.jpg

Xiongtao Ruan


[email protected]
Assistant Project Scientist
Advanced Bioimaging Center
Department of Molecular and Cell Biology
University of California, Berkeley


I’m an Assistant Project Scientist in the Advanced Bioimaging Center at UC Berkeley, working with Drs. Gokul Upadhyayula and Eric Betzig. In May 2019, I obtained my Ph.D. in Computational Biology advised by Dr. Robert F. Murphy at Carnegie Mellon University.

I develop technologies that accelerate biological discovery by combining advanced microscopy with computational innovation. I helped develop MOSAIC, a microscope that generates massive datasets, and created PetaKit5D, a platform for real-time, petabyte-scale image processing. Using these tools with laser-degradable expansion microscopy, we produced the first nanoscale images of entire mouse olfactory bulbs, revealing patterns of neurodegeneration. This integrated approach enables large-scale, high-resolution mapping of complex biological systems and is broadly applicable across neuroscience, cancer research, and developmental biology.

Education and employment


Selected publications

  1. A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms
    Fu, T.*, Liu, G.*, Milkie, DE.*,  Ruan, X.*, Gorlitz, F., Shi, Y., Ferro, V., Divekar, NS., Wang, W., York, HM., Kilic, V., Mueller, M., Liang, Y., Daugird, TA., Gacha-Garay, MJ., Larkin, KA., Adikes, RC., Harrison, N., Shirazinejad, C., Williams, S., Nourse, JL., Sheu, S., Gao, L., Li, T., Mondal, C., Achour, K., Hercule, W., Stabley, D., Emmerich, K., Dong, P., Drubin, D., Liu, ZJ., Clapham, D., Mumm, JS., Koyama, M., Killilea, A., Bravo-Cordero, JJ., Keene, CD., Luo, L., Kirchhausen, T., Pathak, MM., Arumugam, S., Nunez, JK., Gao, R., Matus, DQ., Martin, BL., Swinburne, IA., Betzig, E.#, Legant, WR.#, and Upadhyayula, S.#
    bioRxiv, 2025
  2. 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
  3. 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
  4. 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
  5. Evaluation of methods for generative modeling of cell and nuclear shape
    Ruan, X., and Murphy, RF.
    Bioinformatics, 2019