Hyperspy Workshop- 2021



This workshop took place Monday to Friday (April 19th to 23rd) 2021 on Zoom.

Phillip Crout (University of Cambridge)
Magnus Nord (NTNU, Norway)
Francisco de la Peña (University of Lille)
Eric Prestat (University of Manchester- SuperSTEM)
Timothy Poon (Diamond Light Source)
Thomas Slater (ePSIC - Diamond Light Source)




Workshop Software Platform

We will be running the workshop on Google Cloud Platform. Please visit the following link:


and request to join this Google Group (you will need a Google account to join). This would then give you access to the cluster on GCP. Once you start the server, you will have to clone a github repository that contains all the notebooks for the workshop. The data required for the workshop should appear on your /home directory from the start.

For Q&A both before and during the workshop we will be running a Slack channel.


Installation guide- Conda installation

These instructions are provided to enable you to have your personalised hyperspy (and other packages covered in this workshop) installed on you local machine. Having the installation done through this route allows you to have these packages updated independent of each other, in case there is a new release in future.

Please follow the steps below for the installation:

  • Install Python 3.7 from Anaconda

  • Open an Anaconda Prompt Terminal and create a new environment by running:

    1 conda create --name hyperspy_env python=3.7
  • Activate the above environment by:

    1 2 WINDOWS: activate hyperspy_env LINUX, macOS: source activate hyperspy_env
  • Install the packages by running the following commands:

    1 2 3 4 5 6 7 8 conda install hyperspy -c conda-forge conda install -c conda-forge pyxem conda install -c conda-forge atomap conda install -c conda-forge particlespy conda install -c conda-forge jupyterlab conda install -c conda-forge notebook conda install -c conda-forge ipympl python -m ipykernel install --user --name=hyperspy_env

Please note that given the number of participants in this year’s workshop we may not be able to provide technical support for local installations.





To test your installation, from the same prompt, run:

1 jupyter notebook

This would open a Jupyter notebook launcher in your web browser. Under Notebook select Python 3 button to open a new notebook. Copy this code to the first cell and run (press shift + enter). If the installation is correct you should not get any error messages (Note that you may get a Warning about pyOpenCl that can be ignored.).

1 2 3 4 5 %matplotlib qt5 import hyperspy.api as hs import pyxem as pxm import atomap.api as am import ParticleSpy.api as ps





Workshop Notebooks and Presentations

We will gradually make the Jupyter notebooks, example datasets and presentations available here to download. In the meantime, we will be updating this github repository:



Notebooks and Presentations

Notebooks can ge accessed here: https://github.com/ePSIC-DLS/Hyperspy_Workshop_2021

HyperSpy Talk

Curve Fitting

Machine Learning

EDX Data Analysis

HyperSpy Community