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DOI: 10.22184/1993-8578.2021.14.1.62.67
Nowadays, virus research has become an especially urgent task. Scanning probe microscopy allows one to obtain unique information about the morphology and properties of viruses, which are inaccessible by other methods, and may explain, for example, the ability of viruses to withstand many external environmental factors and adapt to external conditions. Mechanical and geometrical properties, adhesion, tendency to aggregation, ability to crystallize can be obtained using the probe microscopy. In these studies, specialized software is an important tool for processing and analyzing the results obtained.
Nowadays, virus research has become an especially urgent task. Scanning probe microscopy allows one to obtain unique information about the morphology and properties of viruses, which are inaccessible by other methods, and may explain, for example, the ability of viruses to withstand many external environmental factors and adapt to external conditions. Mechanical and geometrical properties, adhesion, tendency to aggregation, ability to crystallize can be obtained using the probe microscopy. In these studies, specialized software is an important tool for processing and analyzing the results obtained.
Теги: morphology of viruses scanning probe microscopy viruses вирусы морфология вирусов сканирующая зондовая микроскопия
FEMTOSCAN ONLINE SOFTWARE IN VIRUS RESEARCH
Nowadays, virus research has become an especially urgent task. Scanning probe microscopy allows one to obtain unique information about the morphology and properties of viruses, which are inaccessible by other methods, and may explain, for example, the ability of viruses to withstand many external environmental factors and adapt to external conditions. Mechanical and geometrical properties, adhesion, tendency to aggregation, ability to crystallize can be obtained using the probe microscopy. In these studies, specialized software is an important tool for processing and analyzing the results obtained.
The article addresses in detail how to process the images obtained after scanning. In most cases, the perception and interpretation of the obtained results largely depend on correct visualization [1].
The resulting image can have a general tilt or a general curvature caused by temperature drift or non-linearity of the piezoceramic manipulator. The first thing to do when processing an image in FemtoScan Online software is to remove the average slope calculated by the least squares method or using splines.
There is often a noise component in the image. In order to eliminate it, you can use a useful option – alignment of all lines of the image to the average level. This option replaces the value at each point with the arithmetic mean of all points in its immediate vicinity. This method is suitable for removing noise and glitches along scan lines. Line averaging can be applied to the entire image or a selected area.
Using the Section tool, you can get a relief profile along the selected line and estimate the elevation difference (Fig.1).
Measurement of angles, distances, lengths of broken lines
Using the ruler, you can measure the distance or size of the object of interest, and also use the marks to count the number of particles in the field of view (Fig.2 and 3). The software can process data obtained using other types of microscopy, for example, transmission electron microscopy.
When working with an image, you can use various types of filtering. Side illumination allows you to increase the contrast of the image and make small details more pronounced without losing information about large objects (Fig.5).
The Wiener filter will filter the selected area with a mask of an arbitrary size. This command allows you to get rid of random noise in the image. Median filtering allows you to smooth out sharp outliers on the image and, unlike averaging, preserves steps. The Median X filter uses a 3 × 3 pixel X configuration as a mask (Fig.6).
Surface Roughness Analysis
In the simplest case, the roughness (namely, Ra, the average roughness) is the arithmetic mean deviation of the cross-sectional profile from the straight line of its total slope. In order to determine the average surface roughness, several sections are built. In the Parameters dialog box, you can select the number of sections and the distance between sections, the length and angle of inclination to the horizontal (Fig.7). The tilt angle can be set manually. If the surface is a layered structure, it is better to use automatic angle detection.
You can also use the function of grain analysis, it allows you to determine the true geometric characteristics of objects on the surface - area, height, perimeter, and volume (Fig.8).
Taking off force curves allows not only to measure the force curve at each point of the surface, but also to actually control interaction of the probe and the sample.
The most interesting and artistic challenge is choosing a color palette and creating 3D images.
Another convenient function is the ability to synchronously move the selected area, detailed image, section area and Fourier image (Fig.9).
FemtoScan Online software recognizes images received in other formats, including microscopes of other companies that are no longer available. The program carries out prepress preparation and image preparation: backlighting, setting colors and fonts, creation of 3D images and videos including a fly over the surface, stereo mode for 3D images and much more [2–9]. ■
The research was carried out with the financial support of the Russian Foundation for Basic Research and the Royal Society of London No. 21-58-10005, the Russian Science Foundation, project No. 20-12-00389, and the Russian Foundation for Basic Research, project No. 20-32-90036.
Nowadays, virus research has become an especially urgent task. Scanning probe microscopy allows one to obtain unique information about the morphology and properties of viruses, which are inaccessible by other methods, and may explain, for example, the ability of viruses to withstand many external environmental factors and adapt to external conditions. Mechanical and geometrical properties, adhesion, tendency to aggregation, ability to crystallize can be obtained using the probe microscopy. In these studies, specialized software is an important tool for processing and analyzing the results obtained.
The article addresses in detail how to process the images obtained after scanning. In most cases, the perception and interpretation of the obtained results largely depend on correct visualization [1].
The resulting image can have a general tilt or a general curvature caused by temperature drift or non-linearity of the piezoceramic manipulator. The first thing to do when processing an image in FemtoScan Online software is to remove the average slope calculated by the least squares method or using splines.
There is often a noise component in the image. In order to eliminate it, you can use a useful option – alignment of all lines of the image to the average level. This option replaces the value at each point with the arithmetic mean of all points in its immediate vicinity. This method is suitable for removing noise and glitches along scan lines. Line averaging can be applied to the entire image or a selected area.
Using the Section tool, you can get a relief profile along the selected line and estimate the elevation difference (Fig.1).
Measurement of angles, distances, lengths of broken lines
Using the ruler, you can measure the distance or size of the object of interest, and also use the marks to count the number of particles in the field of view (Fig.2 and 3). The software can process data obtained using other types of microscopy, for example, transmission electron microscopy.
When working with an image, you can use various types of filtering. Side illumination allows you to increase the contrast of the image and make small details more pronounced without losing information about large objects (Fig.5).
The Wiener filter will filter the selected area with a mask of an arbitrary size. This command allows you to get rid of random noise in the image. Median filtering allows you to smooth out sharp outliers on the image and, unlike averaging, preserves steps. The Median X filter uses a 3 × 3 pixel X configuration as a mask (Fig.6).
Surface Roughness Analysis
In the simplest case, the roughness (namely, Ra, the average roughness) is the arithmetic mean deviation of the cross-sectional profile from the straight line of its total slope. In order to determine the average surface roughness, several sections are built. In the Parameters dialog box, you can select the number of sections and the distance between sections, the length and angle of inclination to the horizontal (Fig.7). The tilt angle can be set manually. If the surface is a layered structure, it is better to use automatic angle detection.
You can also use the function of grain analysis, it allows you to determine the true geometric characteristics of objects on the surface - area, height, perimeter, and volume (Fig.8).
Taking off force curves allows not only to measure the force curve at each point of the surface, but also to actually control interaction of the probe and the sample.
The most interesting and artistic challenge is choosing a color palette and creating 3D images.
Another convenient function is the ability to synchronously move the selected area, detailed image, section area and Fourier image (Fig.9).
FemtoScan Online software recognizes images received in other formats, including microscopes of other companies that are no longer available. The program carries out prepress preparation and image preparation: backlighting, setting colors and fonts, creation of 3D images and videos including a fly over the surface, stereo mode for 3D images and much more [2–9]. ■
The research was carried out with the financial support of the Russian Foundation for Basic Research and the Royal Society of London No. 21-58-10005, the Russian Science Foundation, project No. 20-12-00389, and the Russian Foundation for Basic Research, project No. 20-32-90036.
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