Lewys Jones's Research

MatLab Software

As part of my ongoing doctoral studies a series of MatLab image analysis / processing codes have been developed all themed around high resolution dark field STEM imaging. These are each summarised below with links to their dedicated pages.

Jitterbug Beetle

Jitterbug v3.6

Jitterbug is a piece of code that attempts to remedy some of the most common imaging defects found in STEM images, including:

  • Scan noise,
  • Specimen drift, and
  • Probe wobble (both horizontal & vertical).

In tests the current version yields SNR improvements of up to 42% and resolution improvements of up to 10% by correcting images in post-processing. Jitterbug is availble to download for free for academic/non-commercial use. A full-length paper describing the technique is available here.

Mountain Climber

Ranger v2.2

Ranger is a peak finding algorithym designed to identify features (usually atoms / atomic-columns) in dark-field STEM electron micrographs. This automated MatLab™ routine is designed to be self-optimising and is suitable for crystal-images, edges, grain/twin boundaries and nano-particles. Ranger is available for free download for academic / non-commercial use.


NEW: Absolute Integrator v1.2

Absolute Integrator is a highly automated tool for quantitative HAADF STEM analysis. Using a complimentary annular-detector sensitivity map this code converts HAADF images to units of fractional beam intensity, calibrates image magnification, subtracts amorphous background, identifies the atomic columns and then calculates their total scattering cross-sections. The output from this code is directly comparable with image simulation for thickness / composition analysis.

STEM Probe Icon

Probe Viewer 3D Beta (v0.6)

Probe Viewer 3D is a STEM probe simulation code for the genreation of three-dimensional STEM optical transfer functions (OTFs). It incoporates options for both round and non-round aberrations (up to fifth order), chromatic aberration as well as the effects of finite source size. Probe Viewer 3D can be used to predict the focal-range needed during the acquisition of STEM focal-series intended for reconstruction with the Chrysalis STEM FSR algorithym.

MatLab Software - Coming Soon



Hawkeye is a package dedicated to scrutinising high resolution STEM images. The main use of the present version is the accurate, quantitative measurement of the image resolution, signal to noise ratio (SNR), and signal to background ratio (SBR). Additional functionalities are currently under development including, resolution asymmetry and inter-peak dip.

Hawkeye has proved invaluable in quantifying the performance of various other image processing tools.

Chrysalis and Butterfly photo


Chrysalis is a package of codes which perfoms the ADF STEM focal series reconstruction described in the current work pages. In addition to improving the resolution of such images, by drawing on image information usually lost when capturing only a single image, Chrysalis also improves the signal to noise ratio by up to a factor of ten times that of the raw data. Both a manuscript and presentation which include additional details were presented at EMAG 2011 and are available here.

MatLab Software Users Map

Below you can view the institutions that use some of these image processing tools.

Jitterbug     Absolute Integrator     Ranger     Probe Viewer 3D    

Coming soon: Hawkeye     Chrysalis

Content © 2012 Lewys Jones - layout & design by Vincent Chan