LI Yiming
Research Scientist

Research Interest

Fluorescence microscopy has become the most widely used technique in cellular biology for noninvasive, time-resolved imaging with high molecular specificity. However, the diffraction of light limits the resolution of standard microscopes to ~200 nm, thus preventing detailed analyses of molecular structures. The development of PALM/STORM super-resolution microscopy (SRM) has pushed the boundaries of optical resolution to a few nanometers so that an optical analysis of the nano-biostructures has become possible.  Various labeling techniques, such as genetically encoded tags, immuno-labeling, fluorogenic tags and, for DNA, fluorescence in situ hybridization (DNA-FISH), allow biomolecules of interest to be specifically labeled, even enabling simultaneous visualization of multiple targets through multicolor imaging. Structural information of protein complexes and assemblies, which was previously only accessible to the classical structural biology techniques (EM, NMR, crystallography), can now be studied in situ by specifically labeled fluorescent probes using the existing standard fluorescence microscopes. However, the axial resolution of common 3D SRM is 40 – 70 nm, which cannot resolve many cellular structures, especially not on the level of structural biology. My overall aim is to push the resolution limit of this technique down to <10 nm in all 3D, enabling structural studies of large dynamic protein assemblies inside intact cells.


2010-2015 Ph. D., Biophysics, Karlsruhe Institute of Technology
2009-2010 M. Sc., Medical Physics, Heidelberg University
2005-2009 B.E., Biomedical Engineering, Shanghai Jiao Tong University



2019-present Department of Biomedical Engineering, Southern University of Science and Technology, Research Associate Scientist
2016-2019 European Molecular Biology Laboratory, Heidelberg, Postdoc

2016.02-2016.09 Yale University,Visiting Scholar


Honors and Awards
2013 International Symposium on Biomedical Imaging Travel Grant
2010-2013 Karlsruhe school of optics and photonics fellowship
2016-2019 EIPOD-Marie Curie Postdoc Fellowship



1.Yiming Li, Yu-Le Wu, Philipp Hoess, Markus Mund, and Jonas Ries. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. Biomed. Opt. Express, 6, 2708-2718, (2019)
2. Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer,Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries. Real-time 3D single-molecule localization using experimental point spread functions. Nat. Methods, 15, 367-369, (2018)

3.Yiming Li, Li Shang, G. Ulrich Nienhaus. Super-resolution imaging-based single particle tracking reveals dynamics of nanoparticle internalization by live cells. Nanoscale, 8, 7423-7429, (2016)

4.Yuji Ishitsuka, Natasha Savage, Yiming Li, Anna Bergs, Nathalie Grün, Daria Kohler, Rebecca Donnelly, G. Ulrich Nienhaus, Reinhard Fischer, Norio Takeshita. Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growth. Science Advances, 1, e1500947 (2016)

5.Yiming Li, Yuji Ishitsuka, Per Niklas Hedde, and G. Ulrich Nienhaus. Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization. ACS Nano 7, 5207–5214 (2013)

6.Shuo Chen, Xiaorui Feng, Yiming Li, Chuanqing Zhou, Peng Xi, Qiushi Ren. Software Controlling algorithms for the system performance optimization of confocal laser scanning microscope. Biomed. Signal Process Control 3, 223-228 (2010)

7.Thevathasan, J. V. et al.Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Nat. Methods 16, 1045–1053 (2019).

8.Yongdeng Zhang, et al., Nanoscale subcellular architecture revealed by multicolor 3D salvaged fluorescence imaging. Nature Methods, Accepted.