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:

• Control data structure

• Calibration data structure

Contents

Contents:

• Installation
• Control Module
• Control Configuration
• Calibration Module
• Tutorials for APT Data Processing
• API Reference
• License Information
• Bibliography

Citation

If you use PyCCAPT in your work, please cite the paper [1]. The complete list of references is on the Bibliography page, and machine-readable citation metadata is provided in CITATION.cff at the repository root.

Indices and Tables

• Index

• Module Index

• Search Page