Describe me
Project description
countparticles
Report the number of particles in each class from a run_data.star
file
produced by RELION.
A single-particle cryo-EM reconstruction comes from a set of particle images
corresponding to projections of identical particles in different orientations.
All datasets are heterogeneous, to various degrees, and data analysis involves
classification of particle images. Knowing how many particles contributed to
any given class is important to decide how to follow up after a classification
job. This command-line tool reports a count of particles in each class in a
run_it???_data.star
file from a RELION Class2D or Class3D job. It can also
optionally produce a bar plot of these particle counts.
Acknowledgments
I would not have been able to put this tool together without the
starfile
library.
Installation
$ pip install countparticles
Usage
$ countparticles --help
Usage: countparticles [OPTIONS] <run_data.star>
Report the number of particles in each class from a run_data.star file
produced by RELION.
Options:
-p, --plot Optional. Display a bar plot of the particle counts. This
is most helpful with only a few classes, e.g. for typical
Class3D results (but not for typical Class2D results with
many classes).
-o, --output TEXT Optional. File name to save the barplot (recommended file
formats: .png, .pdf, .svg or any format supported by
matplotlib). This option has no effect without the
-p/--plot option.
-h, --help Show this message and exit.
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