espm: The Electron Spectro-Microscopy Python Library

Documentation Status

The espm package is designed for the simulation and analysis of scanning transmission electron microscopy (STEM) hyperspectral data analysis. Currently it only supports energy dispersive X-ray spectroscopy (EDXS) data but we will try to extend it to electron energy loss spectroscopy (EELS) data in the future. The main components of the package are: - The simulation of STEM-EDXS datasets using espm.datasets which combines espm.weights for the simulation of spatial distributions and èspm.models for the simulation of spectra. - The hyperspectral unmixing of STEM-EDXS spectrum images using espm.estimators. This module contains algorithms to perform non-negative matrix factorization with diverse regularisation (e.g. Laplacian or L1) and contraints (e.g. simplex). - The espm.models module can also be used to perform a physics-guided decomposition of STEM-EDXS datasets.


You can install this package from PyPi using:

$ pip install espm

If you want to develop, please use the option:

$ git clone
$ cd espm
$ pip install cython
$ pip install -e ".[dev]"

Getting started

Try the api.ipynb notebook in the notebooks folder.


The documentation is available at

You can get started with the following notebooks:


If you use this library, please cite the following paper:

title={espm: A Python library for the simulation of STEM-EDXS datasets},
author={Teurtrie, Adrien and Perraudin, Nathana{\"e}l and Holvoet, Thomas and Chen, Hui and Alexander, Duncan TL and Obozinski, Guillaume and H{\'e}bert, C{\'e}cile},

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