Cryo-EM-Refinement

Matlab implementation of TIP 2020 paper: Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM

by: Mona Zehni, Laurene Donati, Emmanuel Soubies, Zhizhen Zhao, and Michael Unser

Dependencies

• GlobalBioIm:
  https://biomedical-imaging-group.github.io/GlobalBioIm/index.html
• ASPIRE: http://spr.math.princeton.edu/

Code structure

• experiments: Contains the main file to run.

• functions: A set of utility functions.

• LinOpCryo: Operators used in cryo-EM SPR.

• volumes: A set of 3D volumes in mrc format.

User manual

• Run RunMe.m to add the paths of all folders and required libraries.
• Navigate to ./experiments/ folder and run main.m. You can change the dataset and the parameters of the experiments.

Compilation of mex files

• Pre-compiled mex files of projection and adjoint of the projection operators are provided in ./LinOpCryo/functions_opt.
• To re-compile these functions, navigate to ./LinOpCryo/mex_files/ and run mex filename.c -o ../functions_opt/.
• To avoid re-writing the provided pre-compiled mex files, the name of the *.c files slightly differ from the name of the pre-compiled mex files. Once you run any compilations, make sure the name of the functions being used in LinOpCryo/LinOpPBTShift.m matches your compiled mex files.

Citation

If you find this repositry helpful in your publications, please consider citing the following papers:

@ARTICLE{zehni2020,
    author={Zehni, Mona and Donati, Laurène and Soubies, Emmanuel and Zhao, Zhizhen and Unser, Michael},
    journal={IEEE Transactions on Image Processing}, 
    title={Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM}, 
    year={2020},
    volume={29},
    number={},
    pages={6151-6163},
    doi={10.1109/TIP.2020.2984313}}
  
@article{donati2018,
    author = {Laurène Donati and Masih Nilchian and Carlos Oscar S. Sorzano and Michael Unser},
    title = {Fast multiscale reconstruction for Cryo-EM},
    journal = {Journal of Structural Biology},
    volume = {204},
    number = {3},
    pages = {543-554},
    year = {2018},
    issn = {1047-8477},
    doi = {https://doi.org/10.1016/j.jsb.2018.09.008},
    url = {https://www.sciencedirect.com/science/article/pii/S1047847718302697},
}