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The FemtoScan Online software allows to process, analyze and create images in scanning probe microscopy, as well as to operate a scanning probe microscope, including remotely via the Internet. FemtoScan Online perceives more than 100 different formats of data developed by both existing and already disappeared companies, microscopes of which are used in laboratories around the world. The software is convenient for analyzing large images, because two images are displayed: an overview with a "sliding" area and an increased detailed view of the content of the "sliding" area. Also in FemtoScan Online you can view 3D images on a stereo monitor. The software is successfully used in educational work in universities, secondary schools and in the Nanotechnology youth innovation creativity center.
Теги: electron microscopy image processing and analysis optical microscopy scanning probe microscopy обработка и анализ изображений оптическая микроскопия сканирующая зондовая микроскопия электронная микроскопия
In 1996, the first version of FemtoScan Online appeared, a software that allows processing, analysis and creation of images in scanning probe microscopy, as well as control of scanning probe microscope, including remotely via the Internet. Currently, this software can be considered as a de facto standard for processing images and data in scanning probe microscopy.
It so happened that almost every company that produced scanning probe microscopes created its own original data recording format. Avoiding the Babylonian confusion of languages was possible thanks to FemtoScan Online, which introduced a certain order in the heterogeneous and unorganized community of scanning probe microscopy. When the developers appear and disappear, the data formats continued to be supported by this software.
In 2016, a well-equipped laboratory of scanning probe microscopy of Professor Yu.L. Lyubchenko at the University of Nebraska Medical Center (USA), which conducts advanced research, bought a JPK microscope with a new data recording format. The problem of image processing was successfully solved by FemtoScan Online thanks to the built-in automatic file converter. Accustomed to convenience does not want to give up on and specialists working in the field of scanning probe microscopy are no exception. Up-to-date scanning probe microscope is becoming a high-performance instrument that produces thousands of tons of byte "ore". Its processing can become an endlessly long and tedious task if there is not a corresponding tool of the highest productivity.
Why did FemtoScan Online become such a tool? "Whoever wants to be first must be last of all and servant of all", says the Gospel of Mark. FemtoScan Online can be servant. Currently, it supports more than 100 different data recording formats from both existing and already disappeared companies, microscopes of which successfully work in laboratories of the world. Among them are Digital Instruments, Veeco, Bruker, Molecular Imaging, NT-MDT, Asylum Research, Advanced Technologies Center [1]. Hardly it will be possible to make one language and one style for different file formats, but it is quite possible to create an effective translator, and it is solved in FemtoScan Online.
Buttons, pop-ups, icons, mouse clicks are essential attributes of any software. The fewer actions required to achieve a given goal, the better for the user. In FemtoScan Online, optimization of such sequences was carried out in close contact with researchers for the majority of operations when processing, analyzing and creation images.
Most of the functions of FemtoScan Online are intuitively understandable. Having received the initial experience of using the software, you can refer to the user manual for a detailed and deep understanding of the program algorithms (Russian version: http://www.nanoscopy.net/downloads/FemtoScan/FsOnlineManual_en.pdf. English version: http: //www.nanoscopy.net/downloads/FemtoScan/FSOnlineManual_en.pdf).
Let's consider some examples of using the FemtoScan Online. Images of large size (more than 512Ч512 measurement points), as a rule, contain a lot of useful information and are simultaneously labor-intensive for processing. In the FemtoScan Online two images are displayed on the monitor: an overview with a "sliding" area (Fig.1a) and an increased detailed display of the content of the "sliding" area (Fig.1b). Moving the selected area (a sliding area marked with a dotted line in the overview frame in Fig.1a), the user sees in the detailed image (Fig.1b) important features of the sample at a preselected magnification. When moving the selected area, the detailed image, the section along the dashed line and the Fourier image are synchronously changed. And you can choose in a detailed image not one, but several sections along different directions. The original and enlarged images can be presented in various digital palettes. This function makes it possible to substantially shorten the analysis time of the experimental data of inhomogeneous surfaces.
The ability to watch 3D images on a stereo monitor is also supported by FemtoScan Online. In stereo mode, you can perform a "survey" of 3D objects, for example, of an E.coli bacterium. To create such a stereo movie in the software, a sequence of 3D images obtained in different angles with different perspective and magnification is selected. Based on these frames, FemtoScan Online, using the smooth turns and scaling, builds a visual series of images for a stereo movie.
One of the important tasks in the field of image processing, not only with respect to probe microscopy, is the recognition of the objects of the shape that the researcher is interested in. The human eye quickly finds an interesting particle of a certain, for example, cylindrical shape in the image, however, to automate this process, clear mathematical criteria are needed. In the case of applying objects on a smooth surface (standard substrates for probe microscopy are mica or graphite), the image has a uniform background in which automatic search is easily realized by mathematical algorithms built into most programs for image processing for optical, electronic and probe microscopy. However, in the case of more complex substrates, for example, of polymer films or amorphous solids, the surface relief elements may have similarities to the particles of interest, and automatic separation of the latter is not always possible. Difficulties arise also in the attempt of statistical processing of parts that are an integral part of the surface. If the eye easily selects areas of the surface containing the objects of investigation on the image, it is not yet possible to create a mathematical criterion for processing.
Fig.3 shows an example of a rather complex sample – tobacco mosaic virus particles (TMV) from an aqueous solution applied to mica. The image contains a significant number of nanometer-scale structures, the shape of which does not correspond to the objects under study. Particles of TMV are a standard sample for the calibration of different types of microscopes, for example, in the Russian Federation such standard sample on a substrate of highly oriented pyrolytic graphite is approved (GSO 10299-2013). The automatic search algorithm successfully finds on the surface of the substrate the particles that are suitable for height (in the left image in Fig.3 they are marked by arrows), but the person's eye sees that of the more than 150 objects found by the program there are only six TMV particles having a cylindrical shape. In such cases, it is convenient to use the function of Analysis of objects (Mathematics/Analysis of objects), which allows you to manually select objects, calculate their spatial characteristics, and analyze them using a histogram. On the left in Fig.3 is an example of analysis of a single object using the Review function (sliding area), the work of which was described above (Fig.1).
FemtoScan Online allows you to easily and quickly create a table of characteristics of the objects of interest. To do this, it first searches for objects of the appropriate size, as shown on the left in Fig.3. Then, moving a sliding window about the size of an object on a large-scale frame (Fig.3 on the left) and pointing it at the particles of interest, we get a series of images of individual objects (Fig.4 on the left), which by clicking on the "Add object" button are immediately recorded in table for statistics. Thus, FemtoScan Online allows you to combine automatic object search with their manual recognition.
FemtoScan Online can be downloaded using the following links:
• http://www.nanoscopy.net/femtoscanonline/en/download (Russian version);
• http://www.nanoscopy.net/femtoscanonline/en/download (English version).
FemtoScan Online is used in educational activities – in workshops for students of higher educational institutions, for example at Lomonosov Moscow State University, as well as in secondary schools in the lessons of additional education. At the Nanotechnology youth innovation creativity center (www.startinnovation.com), the FemtoScan Online software is a key element of several training courses on scanning probe microscopy and biosensors.
The project was supported by the Russian Foundation for Basic Research No. 17-52-560001.
It so happened that almost every company that produced scanning probe microscopes created its own original data recording format. Avoiding the Babylonian confusion of languages was possible thanks to FemtoScan Online, which introduced a certain order in the heterogeneous and unorganized community of scanning probe microscopy. When the developers appear and disappear, the data formats continued to be supported by this software.
In 2016, a well-equipped laboratory of scanning probe microscopy of Professor Yu.L. Lyubchenko at the University of Nebraska Medical Center (USA), which conducts advanced research, bought a JPK microscope with a new data recording format. The problem of image processing was successfully solved by FemtoScan Online thanks to the built-in automatic file converter. Accustomed to convenience does not want to give up on and specialists working in the field of scanning probe microscopy are no exception. Up-to-date scanning probe microscope is becoming a high-performance instrument that produces thousands of tons of byte "ore". Its processing can become an endlessly long and tedious task if there is not a corresponding tool of the highest productivity.
Why did FemtoScan Online become such a tool? "Whoever wants to be first must be last of all and servant of all", says the Gospel of Mark. FemtoScan Online can be servant. Currently, it supports more than 100 different data recording formats from both existing and already disappeared companies, microscopes of which successfully work in laboratories of the world. Among them are Digital Instruments, Veeco, Bruker, Molecular Imaging, NT-MDT, Asylum Research, Advanced Technologies Center [1]. Hardly it will be possible to make one language and one style for different file formats, but it is quite possible to create an effective translator, and it is solved in FemtoScan Online.
Buttons, pop-ups, icons, mouse clicks are essential attributes of any software. The fewer actions required to achieve a given goal, the better for the user. In FemtoScan Online, optimization of such sequences was carried out in close contact with researchers for the majority of operations when processing, analyzing and creation images.
Most of the functions of FemtoScan Online are intuitively understandable. Having received the initial experience of using the software, you can refer to the user manual for a detailed and deep understanding of the program algorithms (Russian version: http://www.nanoscopy.net/downloads/FemtoScan/FsOnlineManual_en.pdf. English version: http: //www.nanoscopy.net/downloads/FemtoScan/FSOnlineManual_en.pdf).
Let's consider some examples of using the FemtoScan Online. Images of large size (more than 512Ч512 measurement points), as a rule, contain a lot of useful information and are simultaneously labor-intensive for processing. In the FemtoScan Online two images are displayed on the monitor: an overview with a "sliding" area (Fig.1a) and an increased detailed display of the content of the "sliding" area (Fig.1b). Moving the selected area (a sliding area marked with a dotted line in the overview frame in Fig.1a), the user sees in the detailed image (Fig.1b) important features of the sample at a preselected magnification. When moving the selected area, the detailed image, the section along the dashed line and the Fourier image are synchronously changed. And you can choose in a detailed image not one, but several sections along different directions. The original and enlarged images can be presented in various digital palettes. This function makes it possible to substantially shorten the analysis time of the experimental data of inhomogeneous surfaces.
The ability to watch 3D images on a stereo monitor is also supported by FemtoScan Online. In stereo mode, you can perform a "survey" of 3D objects, for example, of an E.coli bacterium. To create such a stereo movie in the software, a sequence of 3D images obtained in different angles with different perspective and magnification is selected. Based on these frames, FemtoScan Online, using the smooth turns and scaling, builds a visual series of images for a stereo movie.
One of the important tasks in the field of image processing, not only with respect to probe microscopy, is the recognition of the objects of the shape that the researcher is interested in. The human eye quickly finds an interesting particle of a certain, for example, cylindrical shape in the image, however, to automate this process, clear mathematical criteria are needed. In the case of applying objects on a smooth surface (standard substrates for probe microscopy are mica or graphite), the image has a uniform background in which automatic search is easily realized by mathematical algorithms built into most programs for image processing for optical, electronic and probe microscopy. However, in the case of more complex substrates, for example, of polymer films or amorphous solids, the surface relief elements may have similarities to the particles of interest, and automatic separation of the latter is not always possible. Difficulties arise also in the attempt of statistical processing of parts that are an integral part of the surface. If the eye easily selects areas of the surface containing the objects of investigation on the image, it is not yet possible to create a mathematical criterion for processing.
Fig.3 shows an example of a rather complex sample – tobacco mosaic virus particles (TMV) from an aqueous solution applied to mica. The image contains a significant number of nanometer-scale structures, the shape of which does not correspond to the objects under study. Particles of TMV are a standard sample for the calibration of different types of microscopes, for example, in the Russian Federation such standard sample on a substrate of highly oriented pyrolytic graphite is approved (GSO 10299-2013). The automatic search algorithm successfully finds on the surface of the substrate the particles that are suitable for height (in the left image in Fig.3 they are marked by arrows), but the person's eye sees that of the more than 150 objects found by the program there are only six TMV particles having a cylindrical shape. In such cases, it is convenient to use the function of Analysis of objects (Mathematics/Analysis of objects), which allows you to manually select objects, calculate their spatial characteristics, and analyze them using a histogram. On the left in Fig.3 is an example of analysis of a single object using the Review function (sliding area), the work of which was described above (Fig.1).
FemtoScan Online allows you to easily and quickly create a table of characteristics of the objects of interest. To do this, it first searches for objects of the appropriate size, as shown on the left in Fig.3. Then, moving a sliding window about the size of an object on a large-scale frame (Fig.3 on the left) and pointing it at the particles of interest, we get a series of images of individual objects (Fig.4 on the left), which by clicking on the "Add object" button are immediately recorded in table for statistics. Thus, FemtoScan Online allows you to combine automatic object search with their manual recognition.
FemtoScan Online can be downloaded using the following links:
• http://www.nanoscopy.net/femtoscanonline/en/download (Russian version);
• http://www.nanoscopy.net/femtoscanonline/en/download (English version).
FemtoScan Online is used in educational activities – in workshops for students of higher educational institutions, for example at Lomonosov Moscow State University, as well as in secondary schools in the lessons of additional education. At the Nanotechnology youth innovation creativity center (www.startinnovation.com), the FemtoScan Online software is a key element of several training courses on scanning probe microscopy and biosensors.
The project was supported by the Russian Foundation for Basic Research No. 17-52-560001.
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