Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.
Image Added

This workshop will take 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)

Table of Contents


View file
nameHyperSpy 2021 - Agenda.pdf

nameHyperSpy 2021 - Agenda.pdf

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:

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

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

    Code Block
    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:

Code Block
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.).

Code Block
%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:

HyperSpy Talk

getting started



Introduction to Data Analysis


Curve Fitting


Machine Learning

Big Data & Lazy Signals

EELS Analysis

View file

Curve Fitting

View file

Machine Learning

View file
nameFrancisco - ML.pdf

EDX Data Analysis



HyperSpy Community


HyperSpy Community

View file