As part of my ongoing research 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 v3.6

Jitterbug Photo

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 available to download for free for academic/non-commercial use. A full-length paper describing the technique is available here.

Absolute Integrator v1.6.4


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. Absolute Integrator is available for free download for academic / non-commercial use.

Smart Align v1.6

SmartAlign_LogoSmart Align is a tool for the rigid and/or non-rigid realignment of multiple STEM images. The input images can be bright-field or dark-field and either time-series or focal-series. Smart Align is designed to avoid the common problem of ‘crystal-hopping’ often encountered when re-registering periodic crystal images.

Ranger v2.2

Ranger Photo

Ranger is an automated peak finding algorithm 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 with dark-field (white atom) type contrast. Ranger is available for free download for academic / non-commercial use.

Probe Viewer 3D Beta (v0.6)

probeProbe Viewer 3D is a STEM probe simulation code for the generation of three-dimensional STEM optical transfer functions (OTFs). It incorporates 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 algorithm. Probe Viewer 3D is available for free download for academic / non-commercial use.

MatLab Software Users Map

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

Jitterbug: bug   SmartAlign: SmartAlign_Logo   Ranger: mountains   Absolute Integrator: sigma   Probe Viewer 3D: microscope

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_photoChrysalis is a package of codes which performs 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.