APAV: Python analysis for atom probe tomography

APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and visualization of atom probe tomography experiments, for example:

• Disambiguation of multiple detector events in mass or time-of-flight histograms

• Correlation histograms and molecular dissociation

• Calculation of molecular isotopic distributions

• Read/write common file formats (*.pos, *.epos, *.ato, *.apt, and *.rrng) or simulated data

• Roi primitives for localized analysis

• Interactive visualizations

• Build analyses in the compositional domain (i.e. compositional “grids” with 1st + 2nd pass delocalization)

• Quantify mass spectra using various levels of fitting/background correction

APAV is open source (GPLv2 or greater) and is platform independent. It is written in Python 3 using NumPy to accelerate mathematical computations, and other mathematical tools for more niche calculations. Visualizations leverage pyqtgraph and other custom Qt widgets.

Source code repository: https://gitlab.com/jesseds/apav

Contents

• Download and installation
  • PyPi
  • Git
  • Dependencies
• Getting started
  • Importing data
  • Jupyter Notebooks
  • Interactive plotting
• File formats
  • Positional data
  • APT format
  • Mass ranging data
• Positional data
  • The Roi
  • Basic properties
  • Synthetic data
  • Multiple events
  • Roi subsets
  • Mass/TOF spectra
• Ranging data
  • The Range
  • The RangeCollection
• Isotopic calculations
• Multiple event analysis
  • The CorrelationHistogram
  • The MultipleEventExtractor
• Spectrum analysis
  • Ranged mass spectrum
  • Noise corrected mass spectrum
  • Backgrounds
  • Background collections
  • Local background subtracted mass spectrum
  • Measuring the composition of a precipitate
  • Laser energy dependency
• License
  • Copyright
  • Full license
• API Reference
  • Roi
  • Range
  • Multiple events
  • Mass spectrum
  • Background
  • Models
  • Isotopes
  • Histograms
  • Index

Indices and tables

• Index

• Module Index

• Search Page