Welcome to Atomap’s documentation!

News

2024-10-20: Atomap 0.4.1 released

This is a maintenance release, making Atomap work with NumPy 2.0. It also updates Atomap to use pyproject.toml instead of setup.py.

2024-02-17: Atomap 0.4.0 released

This release is the first to work with the new 2.0.0 version of HyperSpy. The major change is a large improvement in plotting speed, for example sublattice.plot() or sublattice.plot_planes(), thanks to a reimplementation of HyperSpy’s marker functionality. Thanks to Carter Francis for the merge request! There has also been some minor updates of the install instructions, and fixes for deprecation warnings.

About Atomap

Atomap is a Python library for analysing atomic resolution scanning transmission electron microscopy images. It relies in fitting 2-D Gaussian functions to every atomic column in an image, and automatically find all major symmetry axes. The full procedure is explained in the article Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting.

The easiest way to try Atomap is via Binder: introductory Jupyter Notebook. To install Atomap on your own computer, see the install instructions.

Measuring the ellipticity of atomic columns. More info

Mapping the variation in distance between oxygen columns. More information

Atomap is under development and still in alpha, so bugs and errors can be expected. Bug reports and feature requests are welcome on the issue tracker. Contributors are welcome too!

If you publish scientific articles using Atomap, please consider citing the article Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting. (M. Nord et al, Advanced Structural and Chemical Imaging 2017 3:9)

Atomap is available under the GNU GPL v3 license. The source code is found in the GitLab repository.

Contents on this webpage

• Installing
  • HyperSpy bundle
  • Anaconda Python distribution
  • PyPI installation
  • Development version
• Start Atomap
  • Tutorials
• Finding the atom lattice
  • A simple cubic structure
  • Images with more than one sublattice
  • Finding the oxygen sublattice
• Analysing atom lattices
  • Fantasite, the dummy structure
  • The Atom_Lattice object
  • Ellipticity
  • Distance between monolayers
  • Atom distance difference
  • Angle between atoms
  • Integration of atomic columns
  • Line profiles
  • Finding polarization
  • Plotting a pair distribution function
• Dumbbell lattice
  • Dumbbell vector
  • Making the dumbbell lattice
  • Analysing the image
• Several phases
  • Precipitate
  • Matrix
  • Analysing the sublattices
• GUI functionality
  • Selecting atoms with GUI
  • Adding atoms using GUI
  • Toggle atom refine
• Automation of the analysis
  • Finding atom lattices with process parameters
  • Making process parameters
• Examples
  • Dumbbell example
  • Nanoparticle example
  • Precipitate example
  • Perovskite oxide
• Quantification
  • Absolute Integrator
  • Statistical Method
• Working with atomic models
  • Exporting to atomic models
  • Importing atomic models
• Quantify scan distortions
• Making datasets for testing
  • Large amount of atoms
• Plotting for publications
  • Saving specific data
  • Matplotlib
• Various tools
  • Rotating image and points
  • Working with single atom sublattices
• Become a contributor
  • Why contribute
  • What to contribute
  • Version control
  • First steps: setting up git
  • Second steps: Adding something
  • Learn more
• Development guide
  • Testing
  • Style checks
  • Generating the sphinx page
  • Continuous integration
  • Documentation from development branch
• API documentation
  • Classes
  • Modules

• Index

• Module Index

Old news

2023-11-18: Atomap 0.3.4 released

This release has a large performance improvement for the 2D Gaussian refinement, which is especially noticeable for large images with many atoms. A new parameter, nearest_neighbors, has been added to sublattice.construct_zone_axes: increasing it will give more atomic planes. Note: due to a new API-breaking version of HyperSpy (2.0.0), this Atomap release will be the last which will work with the older HyperSpy versions (1.x.x). Thus, the next releases will only work with HyperSpy 2.0.0 or higher, most users should not notice any differences.

2023-5-17: Atomap 0.3.3 released

This is a small maintenance release, fixing some deprecation warning, style issues, and fixing a plotting bug when visualizing vectors.

2022-4-28: Atomap 0.3.2 released

This is a maintenance release, updating Atomap to work with the newly released HyperSpy 1.7.

2021-6-11: Atomap 0.3.1 released!

This is a small release, with one bug fix from Tom Slater, and two performance improvements from Niels Cautaerts. The latter are related to finding the initial atomic column positions, and will especially improve the processing time for large images.

2021-4-23: Try Atomap without having to install anything, via Binder

• Introductory Jupyter Notebook

2021-1-30: Atomap 0.3.0 released!

• Information about the 3D structure of Sublattices can now be added, allowing for 3D atomic models to be “converted” into an Atom_Lattice via the Atomic Simulation Environment, and vice versa. This 3D information can be set manually, or via the intensity for homogeneous structures see statistical method and working with atomic models for more info. Thanks to Tom Slater and Eoghan O’Connell for implementing this!

• The performance of atomic column integration has been greatly improved, atomap.integrate and Atom_Lattice.integrate_column_intensity will be much faster now. Thanks to Thomas Aarholt!

• set_scale() method in Atom_Lattice and Sublattice has been added for easily setting the scale and unit.

• Better support for visualizing Atom_Lattice and Sublattice objects with scaled units. Thanks to Eoghan O’Connell for adding this.

2020-1-29: Atomap 0.2.1 released!

• New method for getting a pair distribution function, see the documentation for more info. Thanks to Tom Slater for implementing this!

• Add a method for getting the local, often high frequency, scanning distortions utilizing the shape of the atomic columns: Quantify scan distortions.

• Improved the progressbar when using Atomap in Jupyter Notebooks. Thanks to Alexander Skorikov!

2019-10-17: Atomap 0.2.0 released!

• Greatly improved documentation, notebook and several new functions for analysing images with dumbbell features, like Si or GaAs.

• New GUI tool for selection a subset of atom positions, making it easier to work on images with several phases.

• Statistical quantification using Gaussian mixture model. Thanks to Tom Slater for implementing this!

• Functions in the Atom_Position class: calculate_max_intensity() and calculate_min_intensity(). Thanks to Eoghan O’Connell for implementing this!

2019-03-05: Atomap 0.1.4 released!

This release includes:

• Functions to find shifts within unit cells, often seen in materials with polarization. This can for example be used to find shifts in B-cations in relation to the A-cations in a perovskite structure: Finding polarization.

• Big optimization in refining the atom positions using centre of mass, which makes it much easier to work with images containing a large number of atoms. For smaller images the improvement is around 5-10 times, while for larger ones it is 1000 times faster. Thanks to Thomas Aarholt for implementing this!

• Similar optimizations to get_model_image(), which is primarily used to generate test data via the Dummy data module. This means generating test data like get_fantasite() is 60 times faster, with even bigger improvements to larger test data. Thanks to Annick De Backer at EMAT for tips on how to improve this!

Another optimization for the Integration of atomic columns functionality is in the pipeline, with a merge request from Thomas Aarholt.

2018-11-26: Atomap 0.1.3 released!

Major features in this release includes:

• A GUI function for adding and removing atoms, which makes it easier to set up the initial atom positions. See Adding atoms using GUI for more information.

• A GUI function for toggling if atom positions should be refined or not, see Toggle atom refine.

• Better handling of hexagonal structures, by adding a adding a vector_fraction parameter to find_missing_atoms_from_zone_vector, thanks to Eoghan O’Connell for the suggestion!

• The addition of mask_radius to the refine functions, which makes it easier to work with non-perodic atom positions, for example Working with single atom sublattices.

2018-06-13: Atomap 0.1.2 released!

This is a minor release, including a signal attribute in Sublattice and Atom_Lattice classes, minor changes in package dependencies and some improvements to the documentation.

2018-03-25: Atomap 0.1.1 released!

The major new features are methods for integrating atomic column intensity and quantifying this intensity in ADF STEM images, see Integration of atomic columns and Absolute Integrator for more info. Thanks to Katherine E. MacArthur for adding this! Other features include tools for rotating atomic positions for plotting purposes (Rotating image and points), and reduced memory use when processing data with many atoms.

2017-11-16: Atomap 0.1.0 released!

We are happy to announce a new Atomap release. It includes a major makeover of the tutorial, start with Finding the atom lattice. New features in this release are methods for finding atomic column intensity, new and simple plotting tools and a module for generating test data.

2017-07-03: version 0.0.8 released!

New features: ability to process dumbbell structures, fitting of multiple 2D Gaussians at the same time, improved background subtraction during 2D Gaussian fitting, and processing of nanoparticles.