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.
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Installation Instructions (Linux/Mac OS X/Windows)
Install Anaconda 64-bit for your platform.
git clone https://github.com/PrincetonUniversity/APPLEpicker-python.git 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/run.py -s particle_size mrc_dir
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
If you want APPLE-Picker to create a JPG image of the result, pass the flag
To see help text, simply pass
You can override more default values by editing the file