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Automatic Particle Picking, a Low-Effort Cryo-EM Framework

This is the Python version of APPLE picker, a particle picker for single-particle cryo-electron microscopy (cryo-EM). For more information on the algorithm, please see the paper.

If you are looking for the MATLAB version, please see the APPLEpicker page.

Make sure to subscribe to important updates, tips and tricks about the APPLE picker.

Installation Instructions (Linux/Mac OS X/Windows)

Install Anaconda 64-bit for your platform.

Next, run

git clone
cd /path/to/git/clone/folder
conda env create -f environment.yml

You're all set! You can now run the APPLE-Picker within your newly created applepicker enviroment:

conda activate applepicker
python /path/to/git/clone/folder/ -s particle_size mrc_dir

where particle_size is the expected size of the particles in pixels and mrc_dir is the folder containing the micrographs. The output files will be placed in a new folder called star_dir in the same parent folder as mrc_dir. You can also specify another output directory using flag -o output_dir.

If you want APPLE-Picker to create a JPG image of the result, pass the flag --jpg.

To see help text, simply pass -h or --help.

You can override more default values by editing the file

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