espm: The Electron Spectro-Microscopy Python Library

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This library contains algorithms to perform non-negative matrix factorization with diverse regularisation (e.g. Laplacian or L1) and contraints (e.g. simplex).

It is specialized for Electron Microscopy applications. It contains code to create artificial Energy dispersive X-ray spectroscopy (EDXS) data and to perform hyperspectral unmixing on EDXS spectrum images.

Installation

You can install this package from PyPi using::

$ pip install espm

If you want to develop, please use the option::

$ git clone https://github.com/adriente/espm.git
$ cd espm
$ pip install cython
$ pip install -e ".[dev]" 

Getting started

Try the api.ipynb notebook in the notebooks folder.

Documentation

The documentation is available at https://espm.readthedocs.io/en/latest/

You can get started with the following notebooks:

• https://espm.readthedocs.io/en/latest/introduction/notebooks/api.html
• https://espm.readthedocs.io/en/latest/introduction/notebooks/toy-problem.html

CITING

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

@article{teurtrie2023espm,
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},
journal={Ultramicroscopy},
pages={113719},
year={2023},
publisher={Elsevier}
}