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Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis
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3.See http://www.imagemet.com for information SPIP, a commercial SPM image processor.
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http://aip.metastore.ingenta.com/content/aip/journal/rsi/84/11/10.1063/1.4827076
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Image of FIG. 1.

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FIG. 1.

A sequence of images from automated STM tip conditioning on the Si(111) 7 × 7 surface, image widths are 128 nm for (a) and (b), and 32 nm for (c)–(e). (a) First scan shows an unstable tip. (b) Less than 7 min into the run, a flat area is detected despite, despite the presence of a step in the scan region. The automation algorithm zooms in for finer tuning. Poor quality atomic resolution is detected (c), as are steps in atomic resolution images (d). After less than 80 min good quality imaging is detected, despite surface contamination being present. SPIW algorithms are used to determine the surface structure and image quality after each image is taken.

Image of FIG. 2.

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FIG. 2.

(a) Raw STM image of Si(111) 7×7 reconstruction. (b) Line-by-line flattening of the same image, resulting in distortion of the surface near contamination. (c) Iterative plane flattening (with masking) of same image using a SPIW algorithm. (Scale bars 6 nm.)

Image of FIG. 3.

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FIG. 3.

(a) 2D schematic of masking procedure. Maxima/minima are marked with red/blue points, their means by solid lines. is the calculated corrugation height, and is the fraction of above/below which features are masked. (b) STM image of Si(111) 7×7 reconstruction flattened using a first order polynomial plane. (c) Resulting mask of high and low areas of (b), using surface corrugations to set threshold height. (d) Result of 5 iterations of flattening non-masked regions, and re-masking. (e) Processed mask of (d). (f) Result of second order polynomial flattening only unmasked peaks in (d). (g) Computer vision image of (f). Cyan points represent atoms, red/blue outlines high/low masked areas. Note that the image is now flat enough that all defects and corner holes are masked. (Scale bars 3 nm.)

Image of FIG. 4.

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FIG. 4.

(a) STM image of Si(111) step edges flattened using a first order polynomial plane, with computer vision overlay of located step edges. (b) Image flattened in SPIW with steps taken into account. (c) Histogram of pixel heights for image flattened with the SPIW step method (red), compared compared to first and second order polynomial plane methods (green and blue, respectively). -heights not yet calibrated, see Sec. II D . (Scale bars 20 nm.)

Image of FIG. 5.

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FIG. 5.

(a) STM image of Si(111) 7 × 7 reconstruction flattened using SPIW mask and flatten routines. (b) Computer vision image of (a) with all well-resolved atoms masked for shape. (c) Zoom of boxed region of (b). (Scale bars 3 nm.)

Image of FIG. 6.

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FIG. 6.

(a) STM image of Si(111) step edge flattened using a first order polynomial plane, with computer vision overlay showing located atoms in cyan. (b) Image constructed such that each pixel height is equal to the height of the nearest located atom, with computer vision overlay of located step edge. (c) Image flattened in SPIW with step taken into account. (d) Histogram of pixel heights for image flattened with the SPIW step method (red), compared to first and second order polynomial plane methods (green and blue, respectively). (Scale bars 6 nm.)

Image of FIG. 7.

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FIG. 7.

(a) and (b) Liquid STM image of quaterphenyl-tetracarboxylic acid and terphenyl benzene assembly on HOPG. (c) and (d) Computer vision image of (a) and (b), respectively, with all well resolved molecules masked for shape. (e) and (f) Zoom of boxed region of (c) and (d), respectively. (Scale bars 10 nm.)

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/content/aip/journal/rsi/84/11/10.1063/1.4827076
2013-11-01
2014-04-17

Abstract

We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure.

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Scitation: Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis
http://aip.metastore.ingenta.com/content/aip/journal/rsi/84/11/10.1063/1.4827076
10.1063/1.4827076
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