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countparticles

DOI

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.

Acknowledgments

I would not have been able to put this tool together without the starfile library.

Installation

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

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.