PyCCAPT: A Modular, FAIR Open-Source Python Package for Atom Probe Control and Calibration

PyCCAPT is an open-source Python package for atom probe tomography (APT) experiment control, calibration, reconstruction, and data processing.

The project follows FAIR data principles and uses an HDF5-based storage model that can include experiment context, detector streams, and calibration outputs in a single interoperable format.

Recommended setup starts with a conda environment and a pip install:

conda create -n pyccapt python=3.11
conda activate pyccapt
python -m pip install --upgrade pip
pip install "pyccapt[full]"

Documentation

This documentation covers:

  • installation and environment setup

  • control runtime architecture and configuration

  • calibration workflows and data structures

  • tutorials for common processing pipelines

  • API reference pages

Most PyCCAPT tabular outputs are represented as Pandas DataFrames, which supports integration with scientific Python workflows.

Control and calibration data structures are documented here:

Contents

Contents:

Bibliography

    1. Gault et al., Atom probe tomography. Nat Rev Methods Primers 1, 52 (2021).

  2. D. W. Saxey, Correlated ion analysis and the interpretation of atom probe mass spectra. Ultramicroscopy 111, 473-479 (2011).

Citation

If you use PyCCAPT in your work, please cite:

@article{monajem2025pyccapt,
  title={PyCCAPT: A Python Package for Open-Source Atom Probe Instrument Control and Data Calibration},
  author={Monajem, Mehrpad and Ott, Benedict and Heimerl, Jonas and Meier, Stefan and Hommelhoff, Peter and Felfer, Peter},
  journal={Microscopy Research and Technique},
  volume={88},
  number={12},
  pages={3199--3210},
  year={2025},
  publisher={Wiley Online Library}
}

Indices and Tables