QEM

Quantitative Electron Microscopy


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Table of Contents

1. About The Project
2. Getting Started
3. Roadmap
4. Contributing
5. License
6. Contact
7. Acknowledgments

About The Project

QEM is inspired by StatSTEM, aiming to provide robust, fast and user-friendly quantification for advanced microscopy. The main usage of QEM is to refine scattering cross-sections, atomic positions and number of atoms for each atomic columns. By building accurate atomic models, we can link the workflow between electron microscopy and computational materials science. The computation is accelerated with GPU parallel computing via JAX.

This repo is currently under heavy development.

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Features

QEM currently support the following features

• Global model-based parameter estimation via gradient descent
• Flexibility of model choices (Gaussian, Lorentzian, Voigt, ect)
• Multi-elemental column refinement with different width
• Atomic column assignment with input crystal structure and spatial mask
• Displacement and strain mapping

You can check the example tutorials in the examples

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Getting Started

To get code running locally, let's first create a conda environment.

conda create -n qem python=3.11
conda activate qem
pip install -e .
cd examples

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Roadmap

TO-DO list

• Model based on Keras to support different backend (Tensorflow, PyTorch, JAX)
• Test the code on Windows
• Improve Gaussian mixture model and selection rule
• Atom counting based on simulated library
• Better peak initization
• Perovskite polarisation, oxygen octahedron tilt and distortion
• Add documentation
• Add tests
• User-friendly GUI

See the open issues for a full list of proposed features (and known issues).

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Contributing

Contributions are what makes the open-source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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License

Distributed under the GPLv3 License. See LICENSE for more information.

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Contact

Zezhong Zhang - [email protected]

Project Link: https://github.com/zezhong-zhang/qem

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Acknowledgments

• Readme page based on Best-README-Template

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