Lukas Grünewald

Lukas Grünewald

he/him

Physicist | Electron Microscopist

GitHub Repositories

This is a continuously updated list of my repositories with a short description.

EM ScaleBarTools

  • Fiji macro toolset to quickly add a scale bar to an image
  • The scale bar size is scaled relative to the image dimensions, independent of the image’s pixel dimensions
  • Options to create a more a visually pleasing scale bar (e.g., automatic re-scaling of the pixel size)

Inkscape: Scientific Figure Template

  • Inkscape is a powerful vector-graphics editor to layout and create scientific figures
  • This template contains subfigure labels, arrow annotations, predefined colors for the color picker, and more!

Manuca (Mean Atomic Number Calculator)

  • Python script to calculate various physical properties of compounds (such as the effective atomic number, compositions in at& and wt%)
  • My first test of running a BinderHub project for quick access and as a demo
  • Can be used to create complicated mixtures of compounds
  • Especially useful in combination with Monte Carlo simulations and other material modelling or just to check EDXS/EELS composition results :-)

EM File Readers

  • List of electron microscopy vendor formats and how to open them with FOSS tools
  • I update the list whenever I work with new instrumentation/new file formats

Jupyter Notebook: Particle Size Distribtution

  • Jupyter notebook for fitting a log-normal (or other) particle size distribution to a measured size metric
  • Will calculate and propagate fitting errors

Jupyter Notebook: Interactive EDS-EELS Comparison

  • A short notebook to explore the differences in energy resolution between EDS and EELS
  • A first test of using JupyterLite with HyperSpy/eXSpy

Jupyter Notebook: EDS Processing

  • Jupyter notebook for advanced data processing of S(T)EM-EDS datasets
  • Powered by HyperSpy/eXSpy
  • Data filtering, cropping, binning, etc.
  • Machine learning: PCA/ICA/NMF/…
  • X-ray peak intensity extraction by simple integration or peak fitting

Jupyter Notebook: Image Denoising with Deep Learning

  • Methods to (batch) denoise electron microscopy images using the deep-learning model by Lobato, Friedrich and Van Aert
  • Reading of TIFFs or other electron-microscopy image formats

EM Stuff

  • My first repository!
  • Collection of code snippets and tools related to electron microscopy