Number of found documents: 650
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Deep learning for magnetic resonance spectroscopy quantification: A time frequency analysis approach
Shamaei, Amirmohammad
2020 - English
Magnetic resonance spectroscopy (MRS) is a technique capable of detecting chemical compounds from localized volumes in living tissues. Quantification of MRS signals is required for obtaining the metabolite concentrations of the tissue under investigation. However, reliable quantification of MRS is difficult. Recently deep learning (DL) has been used for metabolite quantification of MRS signals in the frequency domain. In another study, it was shown that DL in combination with time-frequency analysis could be used for artifact detection in MRS. In this study, we verify the hypothesis that DL in combination with time-frequency analysis can also be used for metabolite quantification and yields results more robust than DL trained with MR signals in the frequency domain. We used the complex matrix of absolute wavelet coefficients (WC) for the time-frequency representation of the signal, and convolutional neural network (CNN) implementation for DL. The comparison with DL used for quantification of data in the frequency domain is presented. Keywords: magnetic resonance spectroscop; quantification; deep learning; machine learning Fulltext is available at external website.
Deep learning for magnetic resonance spectroscopy quantification: A time frequency analysis approach

Magnetic resonance spectroscopy (MRS) is a technique capable of detecting chemical compounds from localized volumes in living tissues. Quantification of MRS signals is required for obtaining the ...

Shamaei, Amirmohammad
Ústav přístrojové techniky, 2020

Determination of thickness refinement using STEM detector segments
Skoupý, Radim; Krzyžánek, Vladislav
2019 - English
Quantitative STEM imaging together with Monte Carlo simulations of electron scattering in solids can bring interesting results about properties of many thin samples. It is possible to determine thickness of a sample, to calculate mass of particles and measure mass per length/area. Appropriate calibration is one of the crucial parts of the method. Even a small error or inaccuracy in detector response to electron beam either blanked or full brings significant error into thickness determination. This problem can be overcome by parallel STEM imaging in more segments of the detector. Comparing more segments gives a possibility to use a signal from different segments for different thicknesses of a sample. Accuracy of individual parts of the detector depends on the captured signal quantity. It is desirable to use such a STEM detector segment that provides the greatest signal change to a unit of thickness. To demonstrate the usage, we used a sample of Latex nanospheres placed on thin carbon lacey film, diameter of the nanospheres was around 600 nm in order to compare the results from different detector segments. Thanks to the known thickness of the sample (calculated from its geometrical shape), it is possible to estimate the optimal acquisition settings and post processing steps with the known and the true state of the sample. Keywords: electron-microscopy; Quantitative STEM; thickness determination; detector segments; Monte Carlo simulation Available at various institutes of the ASCR
Determination of thickness refinement using STEM detector segments

Quantitative STEM imaging together with Monte Carlo simulations of electron scattering in solids can bring interesting results about properties of many thin samples. It is possible to determine ...

Skoupý, Radim; Krzyžánek, Vladislav
Ústav přístrojové techniky, 2019

An appropriate method for assessing hydrogel pore sizes by cryo-sem
Adámková, Kateřina; Trudicová, M.; Hrubanová, Kamila; Sedláček, P.; Krzyžánek, Vladislav
2019 - English
The aim of our work was to examine and describe ultrastructure of the agarose hydrogel and any possible structural concentration dependencies, and to assess the distribution and size of pores of agarose hydrogel in dependence on its concentration. Four concentrations were prepared (0.5 %, 1.0 %, 2.0 % and 4.0 % of dry weight content) and cryo-SEM and turbidimetry methods were executed on wet (original) samples in order to image the ultrastructure and measure the pore sizes within. \nReasonable results were obtained for the wet samples as they were closer to their native state they are usually used for applications in. Cryo-SEM and turbidimetry provided comparable results of pore diameters and allowed to compare pore diameters dependant on the concentrations, moreover, it showed more detailed and realistic structure. Keywords: hydrogelcryo-SEM; agarose; cryo-SEM; freezing methods; image analysis Available at various institutes of the ASCR
An appropriate method for assessing hydrogel pore sizes by cryo-sem

The aim of our work was to examine and describe ultrastructure of the agarose hydrogel and any possible structural concentration dependencies, and to assess the distribution and size of pores of ...

Adámková, Kateřina; Trudicová, M.; Hrubanová, Kamila; Sedláček, P.; Krzyžánek, Vladislav
Ústav přístrojové techniky, 2019

Recent Trends in Charged Particle Optics and Surface Physics Instrumentation. Proceedings of the 16th International Seminar
Mika, Filip; Pokorná, Zuzana
2018 - English
The origins of the seminar “Recent Trends in Charged Particle Optics and Surface Physics Instrumentation” date back into the eighties, when as a part of the isolated “Eastern Bloc”, we were short of English-language books, papers and conferences. In 1990, at the second Seminar, there were as many as 30 participants from 5 countries. The third Seminar in 1992 was moved to hotel Skalský dvur in the Bohemian-Moravian Highlands where it has been held as a biannual meeting ever since.\nThe Seminar takes place in a secluded lakeside hotel surrounded by beautiful nature and calm forests, so all participants have a great possibility to see each other every day and to discuss their topics of interest in more detail. This is a great advantage compared to the huge bustling conferences with their many parallel sections, which are a lively celebration of science but\nsometimes it is difficult to meet there the person with whom you want to discuss a particular scientific topic in more detail.\nFrom the very beginning, the Seminar has been conceived as a meeting devoted more to asking questions not answered yet, than to reporting results. This spirit is usually less present in the introductory presentations and posters but is dominant in the following discussions.\n Keywords: charged particle optics; surface physics; instrumentation Available at various institutes of the ASCR
Recent Trends in Charged Particle Optics and Surface Physics Instrumentation. Proceedings of the 16th International Seminar

The origins of the seminar “Recent Trends in Charged Particle Optics and Surface Physics Instrumentation” date back into the eighties, when as a part of the isolated “Eastern Bloc”, we were short of ...

Mika, Filip; Pokorná, Zuzana
Ústav přístrojové techniky, 2018

Very low energy electron transmission spectromicroscopy
Daniel, Benjamin; Radlička, Tomáš; Piňos, Jakub; Mikmeková, Šárka; Konvalina, Ivo; Frank, Luděk; Müllerová, Ilona
2018 - English
For more than 25 years, Scanning Low Energy Electron Microscopy (SLEEM) has been\ndeveloped at the Institute of Scientific Instruments (ISI), with several commercially available SEMs adapted with a cathode lens for SLEEM use, as well as a dedicated self-built UHVSLEEM setup.\nFor a better understanding of contrast formation at low energies, especially at very low energies below 50 eV, where the local density of states plays an important role, more general knowledge about the interaction of (very) low energy electrons with solids is required. This will be achieved using a newly developed ultra-high vacuum (UHV SLEEM) setup which includes several enhancements compared to other available machines. Data processing is presented in, and processed data will be further used and tested with the Monte Carlosimulation package BRUCE, which is being developed by Werner et al. at TU Vienna. Keywords: low energy scanning electron microscopy; electron microscopy; time of flight; electron energy lost spectroscopy Available at various institutes of the ASCR
Very low energy electron transmission spectromicroscopy

For more than 25 years, Scanning Low Energy Electron Microscopy (SLEEM) has been\ndeveloped at the Institute of Scientific Instruments (ISI), with several commercially available SEMs adapted with a ...

Daniel, Benjamin; Radlička, Tomáš; Piňos, Jakub; Mikmeková, Šárka; Konvalina, Ivo; Frank, Luděk; Müllerová, Ilona
Ústav přístrojové techniky, 2018

Hiding e-beam exposure fields by deterministic 2D pattering
Horáček, Miroslav; Knápek, Alexandr; Matějka, Milan; Krátký, Stanislav; Urbánek, M.; Mika, Filip; Kolařík, Vladimír
2018 - English
The high stability and good current homogeneity in the spot of the e-beam writer is crucial to\nthe exposure quality, particularly in the case of large-area structures when gray-scale\nlithography is used. Even though the deflection field distortion is calibrated regularly and\nbeam focus and beam astigmatism is dynamically corrected over the entire deflection field, we can observe disturbances in the exposed relief.\nRecently, we presented a method that makes use of e–beam exposure imperfection by\nintroducing marginally visible high–frequency diffraction gratings of variable pitch that fill in\nseparate orthogonal exposure fields. The actually presented approach follows up our\nresearch on aperiodic arrangements of optical primitives, especially on the phyllotactic–\nlike arrangement of sub–micron relief optical elements. This approach is extended from the\ndiffraction element arrangement to the higher level of exposure fields arrangements. Keywords: phyllotaxis; electron beam lithography Available at various institutes of the ASCR
Hiding e-beam exposure fields by deterministic 2D pattering

The high stability and good current homogeneity in the spot of the e-beam writer is crucial to\nthe exposure quality, particularly in the case of large-area structures when gray-scale\nlithography is ...

Horáček, Miroslav; Knápek, Alexandr; Matějka, Milan; Krátký, Stanislav; Urbánek, M.; Mika, Filip; Kolařík, Vladimír
Ústav přístrojové techniky, 2018

STEM modes in SEM
Konvalina, Ivo; Paták, Aleš; Mikmeková, Eliška; Mika, Filip; Müllerová, Ilona
2018 - English
The segmented semiconductor STEM detector in the Magellan 400 FEG SEM microscope\n(https://www.fei.com/) is used to detect transmitted electrons (TEs) and allows observing\nsamples in four imaging modes. Two modes of objective lens, namely high resolution (HR)\nand ultra-high resolution (UHR), differ by their resolution and by the presence or absence of\na magnetic field around the sample. If the beam deceleration (BD) mode is chosen, then\nan electrostatic field around the sample is added and two further microscope modes HR + BD\nand UHR + BD, become available. Trajectories of TEs are studied with regard to their angular\nand energy distribution in each mode in this work.\n Keywords: SEM; STEM Available at various institutes of the ASCR
STEM modes in SEM

The segmented semiconductor STEM detector in the Magellan 400 FEG SEM microscope\n(https://www.fei.com/) is used to detect transmitted electrons (TEs) and allows observing\nsamples in four imaging ...

Konvalina, Ivo; Paták, Aleš; Mikmeková, Eliška; Mika, Filip; Müllerová, Ilona
Ústav přístrojové techniky, 2018

Creation of electron vortex beams using the holographic reconstruction method in a scanning electron microscope
Řiháček, Tomáš; Horák, M.; Schachinger, T.; Matějka, Milan; Mika, Filip; Müllerová, Ilona
2018 - English
Electron vortex beams (EVB) were theoretically predicted in 2007 and first experimentally\ncreated in 2010. Although they attracted attention of many researchers, their\ninvestigation takes place almost solely in connection with transmission electron microscopes (TEM). On the other hand, although scanning electron microscopes (SEM) may provide some advantages for EVB applications, only little attention has been dedicated to them. Therefore, the aim of this work is to create electron vortices in SEM at energies of several keV. Keywords: electron vortex beams; scanning electron microscopy; electron diffraction Available at various institutes of the ASCR
Creation of electron vortex beams using the holographic reconstruction method in a scanning electron microscope

Electron vortex beams (EVB) were theoretically predicted in 2007 and first experimentally\ncreated in 2010. Although they attracted attention of many researchers, their\ninvestigation takes place ...

Řiháček, Tomáš; Horák, M.; Schachinger, T.; Matějka, Milan; Mika, Filip; Müllerová, Ilona
Ústav přístrojové techniky, 2018

Locking in on large volume light-sheet microscopy
Vettenburg, T.; Dalgarno, H.I.C.; Nylk, J.; Coll-Lladó, C.; Ferrier, D.E.K.; Čižmár, Tomáš; Gunn-Moore, F.J.; Dholakia, K.; Corral, A.; Rodriguez-Pulido, A.; Flors, C.; Ripoll, J.
2018 - English
Fluorescence light-sheet microscopy is increasingly adopted by developmental biologists to study how cells divide and differentiate to form organs and even entire organisms. The lightsheet microscope differs from a conventional microscope in that the specimen is illuminated by a plane of light orthogonal to the detection axis, thus keeping the out-of-focus areas dark while minimizing any potentially detrimental exposure of the sample. The light-sheet microscope has been found to be the ideal instrument for long-term and non-invasive studies of intact, and therefore three-dimensional, fluorescent samples. Keywords: cellular imaging; fluorescence imaging; light-sheet microscopy Available at various institutes of the ASCR
Locking in on large volume light-sheet microscopy

Fluorescence light-sheet microscopy is increasingly adopted by developmental biologists to study how cells divide and differentiate to form organs and even entire organisms. The lightsheet microscope ...

Vettenburg, T.; Dalgarno, H.I.C.; Nylk, J.; Coll-Lladó, C.; Ferrier, D.E.K.; Čižmár, Tomáš; Gunn-Moore, F.J.; Dholakia, K.; Corral, A.; Rodriguez-Pulido, A.; Flors, C.; Ripoll, J.
Ústav přístrojové techniky, 2018

Silver micro drop structured twice around the earth
Meluzín, Petr; Tryhuk, V.; Horáček, Miroslav; Knápek, Alexandr; Krátký, Stanislav; Matějka, Milan; Kolařík, Vladimír
2018 - English
Planar micro structuring of thin metallic layers allows to achieve required surface properties of metallic layers covering bulk materials. Recently, the arrangement of micro holes or pillars placed around the primary spiral according to a phyllotactic model was presented. This deterministically aperiodic planar arrangement was used for benchmarking purposes of the e-beam writer patterning. This arrangement based on single primary spiral and a variety of derived secondary spirals has several interesting properties. One of them is a very low ratio between the area populated by individual micro elements and the length of the primary phyllotactic spiral. This paper presents analysis of the phyllotactic spiral length and the rising gradient at the spiral outer edge. The practical part of the presented work deals with the patterning of a thin silver layer deposited on the silicon or glass substrates using e-beam pattern generation, lithography techniques and related technologies. An interesting impact of the mentioned spiral properties on the e-beam writing strategies and the exposure ordering strategy are also discussed. Keywords: metallic thin layer; planar surface structure; phyllotactic spiral; e-beam writer Available at various institutes of the ASCR
Silver micro drop structured twice around the earth

Planar micro structuring of thin metallic layers allows to achieve required surface properties of metallic layers covering bulk materials. Recently, the arrangement of micro holes or pillars placed ...

Meluzín, Petr; Tryhuk, V.; Horáček, Miroslav; Knápek, Alexandr; Krátký, Stanislav; Matějka, Milan; Kolařík, Vladimír
Ústav přístrojové techniky, 2018

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