Developments in scan strategies for high-speed and low-dose microscopy

Session

Poster Session One

Authors

Jonathan Peters (1, 4), Grigore Moldovan (2), Tiarnan Mullarkey (1, 3), Lewys Jones (1, 4, 3)

Affiliations

1. Advanced Microscopy Laboratory, Trinity College Dublin
2. point electronic
3. Centre for Doctoral Training in the Advanced Characterisation of Materials, AMBER Centre
4. School of Physics, Trinity College Dublin

Keywords

STEM custom scan, dose efficiency

Abstract text

Fundamental limitations in imaging speed and dose delivered to the sample arise from the strategy, or the control logic, employed to scan the beam on the sample. Whilst an idealised scan strategy would simply give a simple scan progression from top-left to bottom-right, in practice the electron beam lags behind the control signals and such a basic scan strategy would have too much image distortion for normal operation. Practical scan strategies use various forms of automatic flyback corrections (i.e. hidden beam motion, or pre-scan), which reduce distortions at slow speeds at the expense of dose - scan hysteresis is always manged by the microscope control system even if not shown in output images. However, scan speeds beyond a few frames per second are required for new areas in microscopy, such as in-situ experiments, where not only that the time required for flyback corrections is prohibitive, but also the dose waisted is unaffordable. Emerging modular, reconfigurable, and reprogrammable scan control does now allow for advanced scan strategies, much beyond the automatic flyback approach [1, 2].  Here we demonstrate serpentine scan patterns in order to increase framerate and improve dose efficiency.

 

A flyback scan strategy follows the basic top-left to bottom-right approach at the expense of added hidden beam motion for each line and frame return, added wait time at each line and frame start, and added hidden beam motion before acquisition on each line. At slow frame rates, time spent for these hidden motions and wait time is not a significant proportion of the time per frame, however at higher frame rates time spent on flyback is a more significant proportion of the acquisition time. Fast scan speeds also necessitate increased flyback time as more hidden motion is required to compensate for higher distortions at higher scan speeds. For these higher frame rates, it’s therefore useful to remove the hidden motion before acquisition on each line and instead introduce image processing to correct for the unavoidable scan distortion [3]. At even higher frame rates however, scan control is completely lost as the large scan steps at end of lines cause large and uneven scan distortions too different from the intended scan geometry. 

 

A serpentine scan strategy is implemented here in order to retain beam control at these high frame rates, as it reverses scan direction between successive lines and frames and therefore avoids the difficult large scan steps at line and frame ends. A Python script has been developed to calculate the serpentine pixel coordinates, and to upload them into the scan controller as a list of pixel map. The scan job was then run real time by a point electronic GmbH TEM scan controller on a TFS Titan TEM, and image data returned to the Python script for saving. Image processing is now always required, as image data formats are defined for a top-left to bottom-right array, and a look-up table approach has been used here to rearrange pixel values. A scan miss-alignment has been found between successive lines at higher speeds due to the change in scan direction, which was corrected in image processing using non-rigid registratio. It will be shown further that this scan distortion can be minimised with either an added wait time after each scan direction change, or by varying the dwell time per pixel such as the beam scan is accelerated at the start and/or slowed down at the end of each line.

References

[1] Velazco A, Nord M, Béché A, Verbeeck J., Ultramicroscopy 215 2020

[2] Sang X, Lupini AR, Ding J, Kalinin SV, Jesse S, Unocic RR., Scientific Reports 7 2017

[3] Mullarkey T, Peters J J P, Downing C, Jones L, Microscopy and Microanalysis 28 2022