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.
This tool was tested with star files produced by RELION-3.1.0. Earlier versions of RELION are not supported.
I would not have been able to put this tool together without the
starfile library.
I recommend to install this tool in a dedicated conda environment. You can
create one like so (replace ENV_NAME with the name you want to give to this
environment):
$ conda deactivate
$ conda create --name ENV_NAME python=3.9
$ conda activate ENV_NAME
Once the conda environment is active, you can install the tool with the following command:
$ pip install countparticles
$ 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.