Microscopy Software Suite - Isis Project No 7869 & 7981

Jitterbug and Chrysalis; a suite of software for processing scanning transmission electron microscopy (STEM) images.

Jitterbug

The purpose of the software is to remove image distortions introduced by the recording instrument in situations where the recording probe or sample are subject to instability.

High resolution scanning transmission electron microscopes are required to operate in rooms where limited vibration and temperature changes occur, and electromagnetic or sound waves are present. The probes are steered back and forth in straight lines by electromagnetic coils, and the probe can drift slightly during the course of scanning an object.

To remove random misalignment, the similarity between an image row and its neighbours is calculated by Jitterbug using a cross-correlation method. This is calculated for a range of row offsets. The row is deemed to be correctly realigned when this parameter is maximised. These offsets are calculated, recorded and finally applied to realign all the rows of an image. To remove the effects of lateral drift, angular deviations in the image power spectrum are analysed and an appropriate compensation applied.

Jitterbug has been developed for the processing of scanning transmission electron microscopy (STEM) images. However, it would be equally applicable to any raster-type serial image collection include scanning electron microscopy (SEM), scanning tunnelling Microscopy (STM) and atomic force microscopy (AFM).

Chrysalis

Focal series restoration, shown overlaid on original data.

The Chrysalis suite is a collection of software programs that, when run successively, perform a focal series restoration (FSR) on scanning transmission electron microscopy (STEM) data. The image rocessing technique can facilitate the production (from a focal series) of an image of higher resolution than attainable from a single STEM image, without the requirement for additional hardware.

In the presence of lens imperfections or aberrations, information is transferred in an imperfect way through an optical system. By recording a focal series a sequence of images can be recorded, each of which contains a variation on the equivalent single image record. By surveying this series, the information which is scattered through the images can be extracted and brought back to a single frame.

Software Status

Isis would be interested in hearing from companies who wish to market this software. Please contact the Technology Transfer Manager using the link below.

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