Welcome to Atomap’s documentation!


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!

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.


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

Old news

2019-10-17: Atomap 0.2.0 released!

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.