Report the number of particles in each class from RELION
Report the number of particles in each class from a
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
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
$ 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.
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