openNCEM's Python Package

electron, microscopy, image, diffraction, processing, simulation
pip install ncempy==1.11.0



A collection of packages, scripts, and tools for electron microscopy data analysis supported by the National Center for Electron Microscopy facility of the Molecular Foundry.

Read the documentation:

Installation of the ncempy package

The newest version can be installed using pip:

>> pip install ncempy

To ensure dependencies for the EDS tomography reconstruction are installed:

>> pip install ncempy[edstomo]


The openNCEM collection comes with different components, described below.

openNCEM's python package to provide various algorithms and routines to process or simulate images.
The tools build leveraging the algorithms and routines provided in the libraries/packages. They are subordered by the different problems they address.


Extracts a PNG file from the data in a SER, DM3, or DM4 file. For 3D and 4D files, it tries to extract an image from the middle of the third and forth dimension.


ncempy is dual licensed under GPLv3 and MIT. The io module is the only part released under MIT to improve interoperability with other packages.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see