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Drift corrected EFTEM Imaging

Category: Microscope & GIF
Description: This script offers an automatic and modified acquisiton methode for EFTEM imaging. Conventional acquired EFTEM images with exposure times above one minute tend to be blurry because of the specimen spatial drift. To alleviate the blurring of the images caused by the drift, this script takes several EFTEM images with a shorter exposure time (sub-images) and merges these sub-images afterwards. To correct for the spatial drift between these sub-images, elastically filtered images are acquired between two subsequent sub-images. These elastically filtered images are used for spatial drift correction based on the cross-correlation method. The gathered drift information between two elastically filtered images is used to drift-corrected the sub-images automatically and merge them afterwards. A reduction of the field of view can be avoided by using the Image Shift function of the microscope for active drift correction during the measurement. Artifacts that are caused by prominent outliers in the dark reference image are suppressed by calculating the dark reference image from three images. Removal of outliers from the sub-images is available as an option. Furthermore, it is possible to drift-correct the full set of EFTEM images already during the acquisition to simplify the post-processing for elemental mapping. Known issues: Because the DM commands for the change of the energy-loss differ between different versions the script might prompt an error when started. For this case the other known commands are available in the respective sub-routines as comments.
Comments: The first version of this script was written for and tested with a ZEISS Libra 200 FE TEM, the latest version ran successfully with a Jeol JEM-ARM200F. This script is related to the publication: T. Heil, H. Kohl, Optimization of EFTEM image acquisition by using elastically filtered images for drift correction, Ultramicroscopy 110 (2010) 748-753
Acknowledgements: For the sobel filter: Script to calculate the Sobel derivative of an image. S. Paciornik Dec 2001 version 2.0 modified by D. Mitchell,, March 2003 The methode to translate the cursor position to image coordinates is copied from the Measure_Angles_DM script written by D. Mitchell Feb 2003 Bernd Kraus from Gatan for the information about the Energy Filter commands
Script version: 5.0
DM/GMS version: 3.20
Hardware: Jeol JEM-ARM200F
Script written as a function: No
Source: Show code
Download Source Code: Download