sizepicker

Density-based cryo-ET particle picker.

Fork of cet_pick_size by the Bartesaghi Lab using more recent Python and some convenience features.

How it works

Run as sizepicker input_files_*.mrc output_folder.
Full help via sizepicker --help.

1. The tomogram will be low-pass filtered to half the particle radius, controlled by --radius. The pixel size is automatically determined from the mrc header, or given via --angpix. The filtered tomogram is written to the output folder.
2. A contamination mask is created for each tomogram:
   • The tomogram is binned to speed up processing (set by --contamination-binning).
   • If --gaussian is passed, a low-pass filtered version of the tomogram is used to flatten the background (controlled by --sigma_cont).
   • Everything that is more dense than n*SD below mean (set by --stdtimes_cont) is considered contamination.
   • This is smoothed, small patches are removed (set by --minsize_cont), holes are removed and the mask is dilated (set by --dilate_cont).
   • The contamination mask is also written to the output folder.
3. Local minima outside the contamination mask are picked, in a local neighborhood of --radiustimes * particle radius. If --inhibit is passed, a slightly more refined algorithm is used, usually giving more picks. Only coordinates within the --detection_z voxels around the center are considered.
4. Subvolumes are extracted from the lowpass-filtered tomogram and z-projected. Only picks, where the SD within the particle is --stdtimes_pick * SD above the mean particle density SD are retained. Additionally, only particles with a higher foreground SD than background SD are kept, unless --remove_edge is passed.
5. XYZ coordinates of the retained picks are written to the output folder.

Design changes vs. reference implementation:

• added ability to loop over several tomograms
• using mrcfile to parse tomograms, removing requirement for Python 3.6.
• using click for CLI
• removed --binning parameter, instead read pixel size out of header
• --sigma_cont is now given in A rather than px
• choice of a few of the default values changed

Installation

Install via: pip install "git+https://github.com/bwmr/sizepicker.git"

Requires newstack from the IMOD package to be on $PATH (it is only used for lowpass-filtering, this requirement will be removed in future versions).

Reference

The paper below describes the original implementation:

journal = {Journal of Structural Biology: X},  
volume = {10},  
pages = {100104},  
year = {2024},  
issn = {2590-1524},  
doi = {https://doi.org/10.1016/j.yjsbx.2024.100104},  
url = {https://www.sciencedirect.com/science/article/pii/S2590152424000096},  
author = {Weisheng Jin and Ye Zhou and Alberto Bartesaghi}