https://github.com/ercius/openncem

A collection of packages and tools for electron microscopy data analysis supported by the National Center for Electron Microscopy facility of the Molecular Foundry
https://github.com/ercius/openncem

Last synced: 2 months ago
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A collection of packages and tools for electron microscopy data analysis supported by the National Center for Electron Microscopy facility of the Molecular Foundry

• Host: GitHub
• URL: https://github.com/ercius/openncem
• Owner: ercius
• License: gpl-3.0
• Created: 2016-11-19T00:05:28.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2024-12-03T00:48:22.000Z (7 months ago)
• Last Synced: 2025-04-04T05:45:56.382Z (2 months ago)
• Language: Jupyter Notebook
• Size: 89.5 MB
• Stars: 62
• Watchers: 10
• Forks: 28
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
========

openNCEM

========

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: https://openncem.readthedocs.io/en/latest/.

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]``

Components

==========

The openNCEM collection comes with different components, described below.

**ncempy**

    openNCEM's python package to provide various algorithms and routines to process or simulate images.

**tools**

    The tools build leveraging the algorithms and routines provided in the libraries/packages. They are subordered by the different problems they address.

Commands

========

**ncem2png**

    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.

License

=======

    ``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 https://www.gnu.org/licenses/.