ePDFsuite

ePDFsuite is a Python toolkit for extracting the electron Pair Distribution Function (ePDF) from Selected Area Electron Diffraction (SAED) images acquired in a transmission electron microscope (TEM).

It provides both a Python API for scripted workflows and an interactive graphical interface built with Streamlit.

See Documentation

What is ePDF?

The electron Pair Distribution Function (ePDF) is a real-space representation of atomic pair correlations, derived from the Fourier transform of the reduced structure factor $F(q)$ extracted from electron diffraction data. It is particularly useful for characterizing the local atomic structure of amorphous, nanocrystalline, and disordered materials.

$$G(r) = \frac{2}{\pi} \int_{q_{\min}}^{q_{\max}} F(q) \sin(qr), dq$$

Features

• Camera geometric calibration using a known crystalline standard (e.g. Au) via pyFAI
• MTF determination from a beamstop image using the slanted edge method
• MTF deconvolution of diffraction images (Wiener filter)
• Automatic beam center recalibration before each integration
• Azimuthal integration of 2D SAED patterns to 1D profiles
• ePDF extraction: background subtraction, scattering factor normalization using Lobato parameterization, and Fourier transform
• Interactive GUI (Streamlit) for interactive parameter tuning
• Support for DM4, DM3, TIFF input formats (via HyperSpy)
• Works with or without a .poni calibration file

Installation

Requirements: Python ≥ 3.8, conda recommended.

# Clone the repository
git clone https://github.com/nicoratel/ePDFsuite.git
cd ePDFsuite

# Create and activate a conda environment
conda create -n epdfsuite python=3.10
conda activate epdfsuite

# Install in editable mode
pip install -e .

Launching the GUI

Once installed, launch the interactive Streamlit application from anywhere:

conda activate epdfsuite
epdfsuite-app

The app opens at http://localhost:8501 in your browser.

See LAUNCH_APP.md for alternative launch methods.

Usage

See Documentation

Notebooks

Project structure

ePDFsuite/
├── src/epdfsuite/
│   ├── ePDFsuite.py          # SAEDProcessor class and extract_epdf function
│   ├── calibration.py        # Geometric calibration from CIF
│   ├── recalibration.py      # Automatic beam center refinement
│   ├── pdf_extraction.py     # Structure factor and PDF computation
│   ├── lobato_scattering.py  # Lobato electron scattering factors
│   ├── filereader.py         # DM4/DM3/TIFF reader
│   ├── utilities.py          # MTF tools, mask drawing
│   ├── camera_library.py     # Known detector configurations
│   └── app_epdfsuite.py      # Streamlit GUI
├── notebooks/                # Example Jupyter notebooks
├── pyproject.toml
├── LAUNCH_APP.md             # GUI launch instructions
└── README.md

Dependencies

License

MIT License — see LICENSE for details.

Author

Nicolas Ratel-Ramond
github.com/nicoratel/ePDFsuite