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• Uninstall previous Miniconda / Anaconda installs
• Install Miniconda from https://conda.io/miniconda.html (restart your MAC)

Once miconda is installed run the following in the terminal (before running the second command you may need to install Node.js, see docs here):

conda install -c conda-forge hyperspy
jupyter labextension install @jupyter-widgets/jupyterlab-manager

• Install pyxem:

conda install -c conda-forge diffpy.structure
pip install https://github.com/pyxem/pyxem/archive/master.zip

• Install atomap and pixstem:

pip install atomap pixstem

To check that all is well with your install, open a Jupyter lab by running:

jupyter lab

Select Python3 under Notebook and copy the following block of code to the first cell in the notebook:

%matplotlib qt
import hyperspy.api as hs
import numpy as np
import atomap.api as am
import pyxem as px
import pixstem as ps

If the installation is correct, you should not get any error messages.