Parakeet is a digital twin for cryo electron tomography and stands for Program for Analysis and Reconstruction of Artificial data for Kryo ElEctron Tomography

Installation

Parakeet can be installed using pip with the following command:

  pip install python-parakeet

NOTE: Because the package needs to be built locally from source and has some external dependencies you may need to ensure your environment is ready before running this command. You need to set the location of the CUDA compiler and possibly G++ and FFTW libraries. For full instructions please see the installation documentation here.

Usage

Parakeet can be used as a suite of command line tools as follows:

  parakeet.config.new -c config.yaml
  parakeet.sample.new -c config.yaml
  parakeet.sample.add_molecules -c config.yaml
  parakeet.simulate.exit_wave -c config.yaml
  parakeet.simulate.optics -c config.yaml
  parakeet.simulate.image -c config.yaml

For full command line usage instructions please see the command line documentation here here. Alternatively, there is a complementary high level Python API which can be seen here.

Documentation

Checkout the documentation for more information!

Notifications

You can receive notifications from the Github discussions by clicking "watch" on this repository.

Issues

Please use the GitHub issue tracker to submit bugs or request features.

Changes

Checkout the changelog for a list of recent changes to parakeet.

Contributions

If you would like to help contribute to profet, please read our contribution guide and code of conduct.

License

Copyright Diamond Light Source and Rosalind Franklin Institute, 2019.

Distributed under the terms of the GPLv3 license, parakeet is free and open source software.