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Hyperspy Workshop- 2025

Hyperspy Workshop- 2025

Speakers:


Carter Francis (Direct Electron - University of Wisconsin-Madison)
Kate MacArthur (Oxford Instruments)
Magnus Nord (NTNU, Norway)
Francisco de la Peña (University of Lille)
Colin Ophus (Stanford University)
Eric Prestat (UKAEA)
Stephanie Ribet (LBL)
Thomas Slater (Cardiff University)
Toma Susi (University of Vienna)
Steven Zeltmann (Cornell University)

 

 

 

Diamond Light Source (ePSIC) organising team:

 

Mohsen Danaie - mohsen.danaie@diamond.ac.uk

Chris Allen

 

Agenda




 

 

 

Workshop Software Platform

We will be running the workshop on your local python installations [Instructions below]. It is crucial that you check your installation ahead of the week of workshop and if you have any issues to get in touch with us.

 

Installation guide- Using the bundle (Preferred route!)

You can use this bundle installer to get all the packages needed for the workshop all at once:

https://hyperspy.org/hyperspy-bundle/

For testing the installation, write click on a location on your machine and select Jupyter lab here and open a Python 3 notebook and try importing the packages as below in testing section.

 

Google Colab

For some of the demos - and as a back up in case your local installation develops an issue - we may run notebooks on Google Colab during the workshop.
Please make sure you have an active Google account for this.
We will share the link to those notebooks during the workshop.

 

Installation guide- Using Miniforge / Mamba (Potentially not as stable as above)

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 from Mambaforge

  • Open a Miniforge terminal. This should look like a regular terminal but with the prompt set to (base)

  • Create a new environment by running:

    conda create --name hyperspy_env python=3.12

  • Activate the above environment by:

    WINDOWS: activate hyperspy_env LINUX, macOS: source activate hyperspy_env

    Now your prompt should read: (hyperspy_env)

  • Install the packages by running the following commands:

    mamba install hyperspy mamba install abtem nglview mamba install pyxem mamba install atomap mamba install particlespy mamba install jupyterlab notebook ipympl mamba install py4dstem pymatgen

Please note that you need to ensure your local installation works ahead of the workshop! Please attend the troubleshooting session on Friday May 30th if in doubt!

 

 

Testing your installation

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

jupyter lab

This would open a Jupyter lab launcher in your web browser (You can choose the default browser here). If you have installed using the Bundle you can right click and select Jupyter Lab here! Under Notebook select Python 3 (ipykernel) 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.).

%matplotlib qt5 import hyperspy.api as hs import pyxem as pxm import atomap.api as am import particlespy.api as ps import py4DSTEM

 

 

 

 

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:

GitHub - ePSIC-DLS/Hyperspy_Workshop_2025: Notebooks used during the 2025 Hyperspy Workshop at ePSIC, Diamond Light Source.

 

Large Data Download link

https://zenodo.org/records/14113591/files/PdCuSiCrystalization-zip.zspy

 

Presentations