The APyT Package: From Raw Atom Probe Data to Three-Dimensional Reconstruction
The APyT package is an advanced, open-source Python framework for evaluating atom probe tomography (APT) data. It offers a suite of modules that automate key steps in APT processing, from mass spectrum calibration to three-dimensional sample reconstruction. Its modular architecture ensures seamless integration with external tools through standardized input/output interfaces, supporting both Linux and Windows environments. Users can import and use each module independently, or integrate them in custom workflows or GUI applications.
For ready-to-use scenarios or testing, a command line interface (CLI) is provided. The CLI offers lightweight wrappers around the core modules, enabling users to process raw measurement data without writing additional Python code. It is particularly useful for exploratory analysis, quick prototyping, and stand-alone usage.
Key features include high efficiency with NumPy and Numba, a low memory footprint, and extensive documentation. The modules are highly automated, requiring minimal user input to achieve accurate results. The package also integrates SQL or local database management for raw measurement data and corresponding metadata.
In addition to its core processing capabilities, APyT includes a growing collection of specialized analysis tools. These currently support tasks such as chemical composition analysis of reconstructed datasets and crystallographic investigations using methods like spatial distribution maps (SDMs). This analysis suite is designed to expand over time, with new tools and techniques added in response to user needs.
Planned future developments include a PyQt-based graphical user interface (GUI) that will unify access to all APyT modules within a single application. This GUI aims to simplify the user experience, making the framework more accessible to researchers unfamiliar with Python while maintaining the flexibility and performance valued by advanced users.
User Guide
Installation
Follow the installation instructions to set up the APyT package on your system and ensure all required dependencies are installed.
Command line interface
The recommended way to interact with the APyT package is through the provided command line scripts. Each script is documented in detail, including available options, expected input/output formats, and usage examples.
Example usage
The APyT package includes a small exemplary measurement file to allow users to explore its functionality without requiring their own raw data. This makes it easy to test the workflow, try out the command line scripts, and familiarize yourself with the graphical interfaces.
For step-by-step instructions on using the example measurement, see the example usage instructions.
Developer Guide
While the command line interface provides convenient, ready-to-use scripts for exploring the capabilities of the APyT package, its modular design allows developers to integrate individual subpackages and modules into custom workflows. Each subpackage is fully documented, enabling programmatic access to core functionality such as file I/O, mass spectrum processing, reconstruction algorithms, and data analysis.
The following list provides an overview of the main APyT subpackages: