Contrast Enhancement of Molecules by Image and Correlation Averaging

Contrast Enhancement of Molecules by Image and Correlation Averaging

More images of the same surface region are aligned and averaged in order to increase the signal to noise ratio. Furthermore, the details of adsorbed hydrocarbon molecules are enhanced by correlation averaging.

A forward and a reverse STM image of the solution-solid interface between coronene in heptanoic acid solution and HOPG were recorded. The adsorbed layer had been heated to 67°C for 3 minutes in pure heptanoic acid, and then cooled to 17°C for measurement.

Both images have been line wise leveled in SPIP™ before further processing.

Two domains are observed in the images - One of coronene lying flat in a hexagonal array, and another (lower left) of coronene standing up with heptanoic acid molecules stretched flat between them.

Reference: H.W. Hipps, Washington State University

Image alignment

Two scans are aligned and averaged.
The offset is 0.5 pixels in y and 5.8 pixels in x.

The white frame shows the selection used for averaging the array in the upper right part of the image

Forward scan

Reverse scan


Correlation Averaging SPM

Correlation averaging

By correlating a selected region with the original image an average with enhancement of the details of the molecular array is obtained.

Templates used for averaging.


3D view

Often, details are better revealed in 3D. The projections are scaled as x:y:z = 1:1:2.


Coronene lying flat


Coronene standing up

Virus Research

Virus Research

Analysis of 2D auto-organized STMV viruses. Reference: Armel Descamps, INSA de LYON / SGM


STMV Viruses

The image exhibits two populations of viruses (STMV) with two discernible diameters.

Detecting repeated structures

Repeated structures can be detected by selecting an Area of Interesting and using the interactive Fourier analysis tools.

Unit cell results

The cell size is calculated automatically when 2 peaks are selected in the Fourier domain.

3D view

3D close-up of the surface exhibiting both viruses of different size.

Molecular Organized System Analysis

Molecular Organized System Analysis

Spectroscopy of surfaces (liquids, solids) in relation with molecular organised systems such as lipids, peptides, proteins, and grafted chains. 3D representation of the brewster and ellipsometric grey levels images obtained with an elli2000 instrument (NFT).


Bernard Despat, Directeur de Recherche, Laboratoire de Physicochimie Moléculaire, Centre National de la Recherche Scientifique


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Micromilling and Analyzing Terraces

Micromilling and Analyzing Terraces

The University of Padova in Italy conducts research to investigate effects of miniaturization on surface generation in micromilling, with a particular focus on generated surface topographies. SPIP™ is used for plane correction, roughness analysis, and quantification, and 3D rendering of milled surfaces exhibiting terraces.

Ball nose micromilling is an interesting technique for the realization of nearly any type of 3D sculptured surface in the mini and micro scale. In particular, the possibility of applying such technique to machining of hardened tool steel makes micromilling a popular choice for micromolds manufacturing. The action of the cutting tool generates a lay characterized by a typical constant wavelength, corresponding to the machining step over with rough sidewalls and traces of chip residual.

Considering the small values of the cutting parameters involved, understanding and evaluating the relevant tool-workpiece materials interaction phenomena require high resolution 3D measuring instruments, such as atomic force microscopy. Other measuring techniques such as stylus profilometry, optical profilometry and stereoscopic scanning electron microscopy were used for comparison.


Reference: Francesco Marinello, PhD at University of Padova

Raw Image of  Milled Surface

Due to scanning artifacts the terraces are tilted.

Plane Correction

The tilt has been corrected using the Plane Correction tool in SPIP™.

Area of Interest (AOI)

The AOI tool has been used to select a single terrace before measuring the roughness.

Detection of terraces

The terraces have been detected by using the particle analysis module.

3D view

The 3D Visualization Studio allows users to render the surface in 3D. In this 1-1-1 view the color bar has been edited assigning a different color to each terrace.