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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In order to showcase Apple-Picker, we created a CodeOcean capsule so you can try the Python version hands on, with your own input, and with different configurations - to your liking. Using CodeOcean you can skip the installation process. You can view the capsule here.
First, verify that your machine has Python 3.5 (or newer) installed by running: python3 -V
Then make sure Pip package manager for Python is installed. Run apt install -y python3-pip --reinstall
As a next step, install Pipenv to easily manage Virtualenv and dependencies: pip3 install pipenv setuptools
If you haven't already, clone the project to your local machine:
git clone https://github.com/PrincetonUniversity/APPLEpicker-python.git
Move into the root folder of the project: cd APPLEpicker-python. You should be able to see the file run.py if you run ls.
Now create a virtual environment for Apple-Picker: pipenv --python 3.5 (or whatever Python version you have).
Install all dependencies: pipenv install.
You're all set! You can now run Apple-Picker within your newly created virtualenv:
pipenv run python3 run.py -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 ourput 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 config.py
If you prefer working directly with pip and requirements.txt,
you can run the following command to extract the dependencies:
pipenv run pip freeze > requirements.txt.
Then run pip install -r requirements.txt.
While running pipenv install, you might run into problems because of missing Linux packages.
Try to install the missing packages using
apt-get install -y libfftw3-3 libfftw3-bin libfftw3-dbg libfftw3-dev libfftw3-doc libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3 libfftw3-quad3 libfftw3-single3
and then run pipenv install again.