EMPyRe - Electron Microscopy Reconstruction

pipeline coverage pypi

EMPyRe is an open source framework for constructing and solving hyperdimensional inverse problems and visualizing the corresponding input and output data. it has its roots in the reconstruction of three-dimensional magnetization distributions from magnetic phase images generated by electron holography but is meant to be extendable for many other problems that are based on forward models that are expressable as a combination of linear subproblems. EMPyRe is purely Python package, so all platforms should be supported.


EMPyRe is available on the Python Package Index and can be simply be installed via pip:

$ pip install empyre

Per default, only the strictly required libraries are installed, but there are a few additional dependencies that will unlock additional capabilites of EMPYRE.

  • io will install the tvtk & HyperSpy packages that are used for loading and saving additional file formats.


    Due to this issue, a pip install of hyperspy is currently not possible. Please use conda to install HyperSpy, instead.

  • fftw will install PyFFTW to speed up Fourier transforms used in some forward models.

  • colors will install the cmocean, whose balance color map is used as a default for the imshow commmand, if available.

  • 3d will install the mayavi package for 3D plotting capabilities.

  • tests will install all dependencies that are needed to test the package (usually not necessary for the average user).

  • all will install all of the dependencies listed above.

You can choose these settings by using, e.g.:

$ pip install empyre[all]


EMPyRe has several dedicated modules which are fully documented here!

  • The fields module provides the Field container class for multidimensional scalar or vector fields and is the fundamental data structure used in EMPyRe.

  • The vis module enables the plotting of Field objects, based on and similar in syntax to the commonly known matplotlib framework.

  • The models module provides tools for constructing forward models that describe processes in Electron Microscopy.

  • The reconstruct module is a collection of tools for solving the inverse problems corresponding to the constructed forward models and diagnostic tools for their assessment.

  • The io module is used to load and save Field objects and the models generated by the models subpackage.

  • The utils module, which houses utility functionality used throughout EMPyRe.

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