SimpliPyTEM - an open source python package for image analysis of electron microscopy images and in situ videos

Session

Early Career Symposium & RMS Early Career Committee AGM

Authors

Mr Gabriel Ing (2), Dr Andy Steward (2), Dr Lorena Ruiz-Perez (1), Prof Giuseppe Battaglia (1)

Affiliations

1. Institute for Bioengineering of Catalan
2. University College London

Keywords

Python 

Image-analysis 

Electron Microscopy

In-situ TEM

Abstract text

Here we present a python library and accompanying graphical user interface (GUI) tailored for processing and analysis of electron microscopy (EM) and in situ EM images. Image processing is commonly necessary following an EM imaging session to do basic functions including image filtering, enhancing contrast and adding a scale-bar. Manually performing these tasks can take a significant amount of time, and many of the methods to automate it are not easy to navigate for beginners. Here we introduce a GUI to automate this process in only a few button clicks. It also allows production of HTML or PDF documents which can act as contact sheets, making post-experimental image evaluation and sharing simple. Combined with this non-coding option, we also introduce  a python library designed specifically to make processing and analysing EM images and in situ EM videos easier for a beginner. The package allows access to the functions most commonly required, including a basic particle analysis module. The library is accompanied by full documentation and tutorials to teach newcomers. We hope that this library can aid users transition to using python for processing and analysing their EM data. As an open source project, we also welcome and encourage contributions from others in the field, allowing effective sharing of computational processes for analysing EM data.