Start Atomap

The first step is starting an interactive JupyterLab environment.

This depends on the installation method:

  • If the HyperSpy bundle was installed, go to HyperSpy-bundle in the start-menu, click Hyperspy-bundle prompt. This will open a command line window, here run jupyter lab.

  • If Anaconda was used, go to Anaconda3 in the start menu, click Anaconda prompt. This will open a command line window, here run jupyter lab.

  • If you’re using MacOS or Linux, run jupyter lab in your Anaconda environment or HyperSpy-bundle environment.

This will open a browser window (or a new browser tab). Click Python 3 (ipykernel), which will start and open an empty Jupyter Notebook.

In the first cell, run the following commands (paste them, and press Shift + Enter). If you are unfamiliar with the Jupyter Notebook interface, see the interactive JupyterLab guide.

%matplotlib widget
import atomap.api as am

If this works, continue to the Tutorials. If you get some kind of error, please report it as a New issue on the Atomap GitLab.


To get you started on using Atomap there are tutorials available. The first tutorial Finding the atom lattice aims at showing how atom positions are found, while Analysing atom lattices shows how this information can be visualized.

The >>> used in the tutorials and documentation means the comment should be typed inside some kind of Python prompt, and can be copy-pasted directly into the Jupyter Notebooks.

Atomap demos

In addition to the guides on this webpage, another good resource is the Atomap demos, which are pre-filled Jupyter Notebooks showing various aspects of Atomap’s functionality. For beginners, the Introduction to Atomap notebook is a good place to start.