HyperSpy workshop 2023

May 22. till May 26.

HyperSpy workshop 2023

This workshop is geared towards electron microscopy users who are interested in HyperSpy for their data analysis.

During this one-week workshop we will cover the basics of data handling in HyperSpy and then provide example work-flowsworkflows for typical datasets that Users acquire at ePSIC. This will include spectroscopy datasets in STEM, i.e. spectrum images with EELS and / or EDXS, and also large 4D-STEM datasets acquired using the Medipix detector on E02. Machine learning toolboxes available within HyperSpy and their application on various data types will also be discussed. We will cover two packages dedicated to 4D-STEM data analysis, PyXEM and py4DSTEM, and a simulation package, abTEM.

We will have ample time for participants to discuss their own specific data analysis questions, with a dedicated “Bring your own data” session towards the end of the workshop.

22/05/20232023-05-22 - 26/05/20232023-05-26
Apply here


The following topics will be covered over the five days:

  • Introduction to HyperSpy
  • Python / hyperspy basics
  • Principal component analysis
  • Electron microscopy image simulation (using abTEM)
  • Energy dispersive X-ay
  • Electron energy loss spectroscopy data analysis 
  • Atomic resolution image analysis (atomap)
  • Electron nano-beam diffraction analysis (PyXEM and Py4DSTEM)


Friday 19th May      
11:00 – 12:00 Optional preparation session (to help with python package
installations and testing ahead of the event)
Monday 22nd May      
13:00 - 13:15 Welcome - Set up
13:15 – 13:45 What is HyperSpy? Talk Francisco de la Peña
13:45 – 14:45 A practical introduction to Python/HyperSpy I Practical  Mohsen Danaie / Eric Prestat
14:45 – 15:00 Coffee break
15:00 – 16:30 A practical introduction to Python/HyperSpy II Practical Mohsen Danaie / Eric Prestat
16:30 – 16:45 Q&A    
Tuesday 23rd May      
10:30 – 11:00 Model Fitting Introduction Talk Francisco de la Peña
11:00 – 12:00 Model Fitting Practical Francisco de la Peña
12:00 – 13:00 Break
13:00 – 13.30 Machine Learning Introduction Talk Francisco de la Peña
13:30 – 14:30 Machine Learning Practical Francisco de la Peña
14:30 – 14:45 Coffee break
14:45 – 16:30 Introduction to abTEM Practical Jacob Madsen
16:30 – 16:45  Q&A    
Wednesday 24th May      
10:30 – 12:00 Big data and lazy signals Practical Magnus Nord
(Including use of dask-distributed dashboard)
12:00 – 13:00 Break
13:00 – 14:15 EELS Analysis in HyperSpy Practical Magnus Nord
14:15 – 14:30 Coffee break
14:30 – 16:30 Introduction to Py4DSTEM  Practical Stephanie Ribet
16:30 – 16:45 Q&A    
Thursday 25th May      
10:30 - 11:00 EDX Analysis Talk Kate MacArthur
11:00 – 12:00 EDX Analysis in HyperSpy Practical Kate MacArthur
12:00 - 13:00 Break
13:00 – 13:45 atomap Practical Magnus Nord
13:45 – 14:30 ParticleSpy Practical Tom Slater
14:30 – 14:45 Coffee break
14:45 – 16:30 SED analysis with PyXem Practical Carter Francis
16:30 - 16:45 Q&A    
Friday 26th May      
10:30 – 11:30 Example Data Analysis with Python libraries Practical  Jacob Madsen
11:30 – 12:00 How to make publication quality plots with matplotlib? Practical Magnus Nord
12:00 – 13:00 Break
13:00 – 13:45 Research / Application talk Talk  TBC
13:45– 14:15 HyperSpy Community / Where to get help! Talk Francisco de la Peña / Eric Prestat
14:15 – 14:30 Coffee break
14:30 – 16:00 Bring Your Own Data! Practical / Zoom
break-out Rooms
16:00 – 16:30 Data analysis workflows at ePSIC Talk Mohsen Danaie
16:30 – 16:45 Q&A – Closing remarks    


  • Francisco de la Peña, University of Lille
  • Carter Francis, University of Wisconsin
  • Katherine MacArthur, Oxford Instruments
  • Jacob Madsen, University of Vienna 
  • Magnus Nord, Norwegian University of Science and Technology
  • Thomas Slater, University of Cardiff 
  • Stephanie Ribet, Lawrence Berkeley National Laboratory
  • Eric Prestat, UK Atomic Energy Authority


Applications for HyperSpy 2023 are now open, and will be closing on Wednesday 3rd May at 17:00 (BTS) 2023.

Apply here Apply here

All applicants will be informed on the result of their application week commencing Monday 8th April 2023.

Please note that places on this workshop are limited. In the case of oversubscription there will be a limit of attendees for each organisation. Participants will be selected on a fair distribution basis across the research groups (where possible at least one person per ePSIC User team will be selected).

Contact us

If you have any questions, please contact events@diamond.ac.uk

Diamond Light Source

Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.

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