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A python wrapper for the non-rigid-registration code match-series

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This is a tool for non-rigid registration, primarily for atomic resolution STEM images, and is a python wrapper of the match-series code developed by B. Berkels. When using this tool, please cite the papers mentioned in that repository.

The goal of match-series is to remove slow and fast scan noise in STEM image stacks by comparing the various images against each other. The output of the code are X and Y deformation fields for each image in the stack. These deformations can then be applied to stacks of images or to EDX/EELS spectum maps that were acquired frame by frame. The goal of pymatchseries is to facilitate the set-up of the calculation and to work with the results in python. It is intended to use this tool mainly semi-interactively in a Jupyter notebook, see the example.

Try it out here: Binder

To install, simply pip install:

$ pip install --user pyMatchSeries

Note that, since it directly tries to call the matchSeries binary in a subprocess, you must compile and/or install match-series on your own. The program is available via conda install:

$ conda install -c conda-forge match-series



  • Significantly simplified the API and made code more future proof
  • Trying out CI/CD pipelines

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