Analysis with Python

Online introduction to Python for electron microscopists

Seeing is believing – if you can trust your eyes and analysis.

Microscopy based studies require validated image analysis as foundation for solid conclusions and understanding of the observed phenomena. Python is an open source programming language with millions of users and developers, enabling analysis of almost any data type. For microscopists, python makes it possible to document and share your method of analysis, which is crucial for the community to learn from each other.

Here we are creating:

  • An introductory course to python for electron microscopists

  • A public databank with real image, videos, and spectra from previous EM experiments and accompanying example analysis you can use to develop and verify your own code

  • A script library, storing open source python scrips, designed to handle and perform EM related data analysis.

In addition we plan to host recurrent workshops, where focus is put on data analysis and coding e.g. in Python. Invited speakers will present and share their code, and we will finish with feedback and discuss it in the forum. This will aid both participants and the presenter in optimizing and developing code for EM analysis.

Over time we hope it will evolve from post-acquisition analysis to more focus on analytics, i.e. real time analysis of the ongoing experiment. If you would like to be involved, please contact us.

Contact persons: Anders Brostrøm and Daniel Kelly.

Content overview

On this site we host:

  • An introductory course on image processing, using Python

  • A library of Python scripts relevant for in situ data treatment.

  • A databank of free images, videos, and spectra from in situ experiments, which can be used to test and develop Python code.


The analysis site is maintained by Daniel Kelly and Anders Brostrøm both from the Technical University of Denmark (DTU).

If you have any comments or feedback, or if you want to contribute to the script library or databank, please do not hesitate to email us.