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A python module for segmentation of STEM images

Project description

Automatic segmentation of STEM images

Automatic segmentation of Scanning Transmission Electron Microscope (STEM) images with unsupervised machine learning

Learning more

If you want to learn more about this project, you may read our manuscript that is not yet completely finished, or our presentation for BiGmax workshop 2020.

Try it now: Binder

Getting Started


python 3, numpy, scipy, scikit-learn, fftw3


via conda, the simplest way, highly recommended

conda install -c conda-forge pystem

via pip

1. First make sure that FFTW3 library is installed 
2. pip install pystem

via source code

1. First make sure that FFTW3 library is installed 
then type commands:
git clone
cd pySTEM
python build
python install --user

How to use

Examples can be found in the examples folder Give it a try right now by simply clicking the 'launch binder' button

Project details

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Files for pystem, version 0.0.25
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