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Frank L.,Institute of Scientific Instruments of the CAS | Mikmekova E.,Institute of Scientific Instruments of the CAS | Mikmekova E.,FEI Company | Lejeune M.,University of Picardie Jules Verne
Applied Surface Science | Year: 2017

Electron-beam-induced deposition of various materials from suitable precursors has represented an established branch of nanotechnology for more than a decade. A specific alternative is carbon deposition on the basis of hydrocarbons as precursors that has been applied to grow various nanostructures including masks for subsequent technological steps. Our area of study was unintentional electron-beam-induced carbon deposition from spontaneously adsorbed hydrocarbon molecules. This process traditionally constitutes a challenge for scanning electron microscopy practice preventing one from performing any true surface studies outside an ultrahigh vacuum and without in-situ cleaning of samples, and also jeopardising other electron-optical devices such as electron beam lithographs. Here we show that when reducing the energy of irradiating electrons sufficiently, the e-beam-induced deposition can be converted to e-beam-induced release causing desorption of hydrocarbons and ultimate cleaning of surfaces in both an ultrahigh and a standard high vacuum. Using series of experiments with graphene samples, we demonstrate fundamental features of e-beam-induced desorption and present results of checks for possible radiation damage using Raman spectroscopy that led to optimisation of the electron energy for damage-free cleaning. The method of preventing carbon contamination described here paves the way for greatly enhanced surface sensitivity of imaging and substantially reduced demands on vacuum systems for nanotechnological applications. © 2017 Elsevier B.V.


KarASek V.,Institute of Scientific Instruments of the CAS | Siler M.,Institute of Scientific Instruments of the CAS | Brzobohaty O.,Institute of Scientific Instruments of the CAS | ZemANek P.,Institute of Scientific Instruments of the CAS
Optics Letters | Year: 2017

This theoretical study based on the coupled dipoles model focuses on the dynamics of two optically bound dielectric spheres of unequal sizes confined in counter-propagating incoherent Bessel beams. We analyzed the relative motion of the particles with respect to each other and defined conditions where they form a stable optically bound structure (OBS). We also investigated the motion of the center of mass of the OBS and found that its direction depends on the particle separation in the structure. Besides the optical interaction between objects, we also considered a hydrodynamic coupling in order to obtain more precise results for moving an OBS. © 2017 Optical Society of America.


Jablonski M.,Institute of Scientific Instruments of the CAS | Jablonski M.,Masaryk University | Starcukova J.,Institute of Scientific Instruments of the CAS | Starcuk Z.,Institute of Scientific Instruments of the CAS
BMC Bioinformatics | Year: 2017

Background: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. Results: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. Conclusions: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra. © 2017 The Author(s).


PubMed | Institute of Scientific Instruments of the CAS and Mendel University in Brno
Type: | Journal: Micron (Oxford, England : 1993) | Year: 2016

This article describes the surface structure of Norway spruce early somatic embryos (ESEs) as a typical culture with asynchronous development. The microstructure of extracellular matrix covering ESEs were observed using the environmental scanning electron microscope as a primary tool and using the scanning electron microscope with cryo attachment and laser electron microscope as a complementary tool allowing our results to be proven independently. The fresh samples were observed in conditions of the air environment of the environmental scanning electron microscope (ESEM) with the pressure from 550Pa to 690Pa and the low temperature of the sample from -18C to -22C. The samples were studied using two different types of detector to allow studying either the thin surface structure or material composition. The scanning electron microscope with cryo attachment was used for imaging frozen extracellular matrix microstructure with higher resolution. The combination of both electron microscopy methods was suitable for observation of native plant samples, allowing correct evaluation of our results, free of error and artifacts.


PubMed | Institute of Scientific Instruments of the CAS, Masaryk University and Charles University
Type: | Journal: Ultramicroscopy | Year: 2016

Single crystal scintillators are frequently used for electron detection in scanning electron microscopy (SEM). We report gadolinium aluminum gallium garnet (GAGG:Ce) single crystalline films as a new perspective scintillators for the SEM. For the first time, the epitaxial garnet films were used in a practical application: the GAGG:Ce scintillator was incorporated into a SEM scintillation electron detector and it showed improved image quality. In order to prove the GAGG:Ce quality accurately, the scintillation properties were examined using electron beam excitation and compared with frequently used scintillators in the SEM. The results demonstrate excellent emission efficiency of the GAGG:Ce single crystalline films together with their very fast scintillation decay useful for demanding SEM applications.


Navratilova E.,Institute of Scientific Instruments of the CAS | Rovnanikova P.,Brno University of Technology
Construction and Building Materials | Year: 2016

The article deals with the evaluation of six brick dusts which were characterized regarding their chemical and mineralogical composition, amorphous phase content, granulometry and specific surface area. The pozzolanic activity was determined by the modified Chapelle test. The analysed brick dusts were used to prepare modified lime mortars in which lime hydrate was replaced by 50% of brick dust. The flexural and compressive strengths of the mortars were determined and pozzolanic activity was calculated from the compressive strengths. The pozzolanic activity of brick dusts is dependent in particular on their amorphous phase content, particle size distribution and specific surface area. Pozzolanic activity increases with increasing amorphous phase content in the brick dusts. Pozzolanic activity has an effect on the strength of modified lime mortars. The higher is the pozzolanic activity value of the added brick dust the higher are the initial and long term strengths of the modified lime mortars. © 2016 Elsevier Ltd.


Kralik T.,Institute of Scientific Instruments of the CAS | Fort T.,Institute of Scientific Instruments of the CAS | Musilova V.,Institute of Scientific Instruments of the CAS | Srnka A.,Institute of Scientific Instruments of the CAS
Refrigeration Science and Technology | Year: 2016

Radiative heat transfer over short distances smaller than wavelengths in the spectrum of radiating surface is enhanced by near field effect. We studied radiative heat transfer between plane parallel surfaces of niobium films (critical temperature 9 K) sputtered on sapphire. The radiative heat flow was 20 times enhanced above the values given by Planck's law (far-field values) in this measurement. Steep decrease of heat flow by a factor of five, caused by transition to superconducting state, was observed in the near field regime. © 2016, International Institute of Refrigeration. All rights reserved.


PubMed | Institute of Scientific Instruments of the CAS, Technical University of Delft and i-Optics
Type: Journal Article | Journal: The Review of scientific instruments | Year: 2016

In this work we present a design of an external optical cavity based on Fabry-Perot etalons applied to a 100 MHz Er-doped fiber optical frequency comb working at 1560 nm to increase its repetition frequency. A Fabry-Perot cavity is constructed based on a transportable cage system with two silver mirrors in plano-concave geometry including the mode-matching lenses, fiber coupled collimation package and detection unit. The system enables full 3D angle mirror tilting and x-y off axis movement as well as distance between the mirrors. We demonstrate the increase of repetition frequency by direct measurement of the beat frequency and spectrally by using the virtually imaged phased array images.


PubMed | Institute of Scientific Instruments of the CAS
Type: | Journal: Magnetic resonance imaging | Year: 2016

A number of Dixon techniques based on fast spin echo (FSE) sequence have been proposed and successfully used in many branches of medicine. Some require only one scan, but most of them need multiple scans and long scan times. This article describes a new fast triple-spin-echo Dixon (FTSED) technique suitable for ultra-high field MRI, in which three specific time shifts are introduced in the echo train; thus, three images with defined water-fat phase-differences (0, , 2) are encoded in the phase of the acquired images without extreme restrictions upon the echo duration. The water and fat images are then calculated by iterative least-squares estimation method. The sequence was successfully implemented at a 9.4T ultra-high field MRI system and tested on a phantom and a rat.


PubMed | Institute of Scientific Instruments of the CAS
Type: Journal Article | Journal: BMC bioinformatics | Year: 2017

Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification.A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background.The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.

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