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Forest condition monitoring in the Czech Republic: Annual report ICP Forests - Data 2003
Boháčová, Ludmila ; Uhlířová, Hana ; Lomský, Bohumír ; Buriánek, V. ; Damašková, J. ; Fabiánek, P. ; Fadrhonsová, V. ; Hejdová, J. ; Novotný, R. ; Neumann, L. ; Šrámek, V.
In the yearbook the methods of assessment and evaluation are presented, and the results at Level I and Level II plots.
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Forest condition monitoring in the Czech Republic: Annual report Forest Focus – Data 2004
Boháčová, Ludmila ; Uhlířová, Hana ; Šrámek, Vít ; Buriánek, V. ; Fabiánek, P. ; Hejdová, J. ; Kapitola, P. ; Lachmanová, Z. ; Lomský, B. ; Neumann, L. ; Novotný, R.
In the yearbook the methods of assessment and evaluation are presented, and the results in the systematic network of plots and intensive monitoring plots (Level I and Level II).
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Forest condition monitoring in the Czech Republic: Annual report Forest Focus/ICP Forests 2005
Boháčová, Ludmila ; Uhlířová, Hana ; Šrámek, Vít ; Buriánek, V. ; Čapek, M. ; Fabiánek, P. ; Hejdová, J. ; Kapitola, P. ; Lachmanová, Z. ; Lomský, B. ; Maxa, M. ; Vortelová, L.
In the yearbook the methods of assessment and evaluation are presented, and the results in the systematic network of plots and intensive monitoring plots (Level I and Level II).
Fulltext: PDF
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Imaging via multimode optical fiber: recovery of a transmission matrix using internal references
Šiler, Martin ; Jákl, Petr ; Traegaardh, Johanna ; Ježek, Jan ; Uhlířová, Hana ; Tučková, Tereza ; Zemánek, Pavel ; Čižmár, Tomáš
Current research of life shows a great desire to study the mechanics of biological processes\ndirectly within the complexity of living organisms. However, majority of practical techniques\nused nowadays for tissue visualization can only reach depths of a few tens of micrometres as\nthe issue obscures deep imaging due to the random light scattering. Several imaging\ntechniques deal with this problems from different angels, such as optical coherence\ntomography, light sheet microscopy or structured light illumination A different and promising strategy to overcome the turbid nature of scattering tissues is to employ multimode optical fibers (MMF) as minimally invasive light guides or endoscopes to provide optical access inside. Although the theoretical description of light propagation through such fibers has been developed a long time ago it is frequently considered inadequate to describe real MMF. The inherent randomization of light propagating through MMFs is typically attributed to undetectable deviations from the ideal fiber structure. It is a commonly believed that this\nadditional chaos is unpredictable and that its influence grows with the length of the fiber.\nDespite this, light transport through MMFs remains deterministic and can be characterized by a transmission matrix (TM) which connects the intensity and phase patterns on the fiber input and output facets. Once the TM is known it can be used to create focus in any desired 3D\ncoordinates beyond the distal fiber facet, see figure 1, and perform e.g. fluorescence based\nlaser scanning microscopy or optical trapping.
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Microscopy of Time Variable Biologic Objects
Uhlířová, Hana ; Kozubek, Michal (referee) ; Peychl,, Jan (referee) ; Chmelík, Radim (advisor)
The subject of the PhD thesis is the application of a transmission digital holographic microscope (DHM) which was designed and constructed in the Laboratory of optical microscopy at the IPE BUT for the research of live cells dynamics. First part of the work is concerned with theoretical description of the microscope imaging properties dependent on the coherence of illumination. It is supplemented with experiments of imaging of a model and a real biological specimen. The following part describes construction modifications and innovations of the microscope and its equipment that enabled the utilization of the microscope for live cells observations. In the experimental part the methodology of live cells preparation and DHM imaging was worked out. The methodology was verified by the observation of cell dynamics during an apoptosis induced by the cytostaticum cis-platinum. Further experiments examined the dynamics of live cells in standard conditions and during a deprivation stimulus. A novel method of holographically reconstructed phase, named \uva{dynamic phase differences}, was set up to evaluate quantitative changes of cell mass distribution during the experiments. Depending on the degree of malignancy and density of cell outgrowth, various schemes of cancer cells behaviour during a specific reaction were revealed using this method. For the quantitative analysis of the DHM phase imaging, a suitable statistical characteristic and an interpretation of the measured data were proposed. Both of them were successfully applied for the comparison of cell motility of two cell types: parental and progeny cell lines. On the basis of the proposed processing, hypotheses describing the reaction mechanism of tumour cells to stress life conditions were established. In the conclusions we summarize our findings and suggestions for the construction and the applications of a new generation of the transmission DHM.
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Coherence-controlled holographic microscope in cell's life cycle research
Křížová, Aneta ; Kozubek,, Michal (referee) ; Uhlířová, Hana (advisor)
The goal of this diploma thesis was using of a coherence-controlled holographic microscope in cell’s life research. A brief history of interference microscopy and it’s applications in biology is described. Also other microscopy techniques routinely used for transparent objects imaging are mentioned and the biology of cell’s life cycle briefly explained. Characteristics describing the shape of a cell were proposed and tested with respect to identification of particular phases of its life cycle. The method of dynamic phase differences was modified in order to distinguish the internal motion of cell’s mass from the movement of the whole cell. Selected characteristics were used to evaluate observations carried out with the holographic microscope and the possibilities of their further applications were depicted. In conclusion, obtained findings were summarized and modifications of microscope construction as well as data-processing software were suggested.
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Coherence-controlled holographic microscope in cell's life cycle research
Bartoníček, Jan ; Chmelík, Radim (referee) ; Uhlířová, Hana (advisor)
The subject of the bachelor thesis is live-cell imaging in a transmitted-light holographic microscope which was designed at the Institute of Physical Engineering BUT and comparing this imaging method with the phase-contrast microscopy. The first part is dedicated to a basic description of used imaging techniques and a cell biology. A description of an experiment preparation follows. In the part dedicated to a data analysis the method of dynamic phase differences is described and the method of growth monitoring is proposed. Both methods were used for the analysis of experiments which are described in the last part of this work. Experiments were focused on acquiring time-lapse data of a cell’s cycle and particularly the mitosis.
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Methodology of Dictyostelium discoideum imaging with the transmission digital holographic microscope
Křížová, Aneta ; Ježek, Jan (referee) ; Uhlířová, Hana (advisor)
The task of this bachelor’s thesis was to image Dictyostelium discoideum with a transmission digital holographic microscope and compare this imaging with a commonly used microscopy technique. This bachelor's thesis is structured into a theoretical part and an experimental part. The theoretical part describes the setting of the transmission digital holographic microscope, basic operation and physical principles of imaging with this microscope. Further the process of image reconstruction and numerical process of phase reconstruction is illustrated. At the end of this part, basic biological characteristics of observed cells of Dictyostelium discoideum are introduced. The experimental part describes the cultivation and preparation of Dictyostelium discoideum for the observations, and further the process of performed experiments. The cells of Dictyostelium discoideum have been imaged in couple experiments by a method of the classical phase contrast. By the transmission digital holographic microscope the cells of Dictyostelium discoideum have been imaged in two mediums. Images captured by the transmission digital holographic microscope were processed by a method of Dynamic phase differences and analysed.
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User programme for imaging and visualization of quantitative phase from the digital holographic microscope
Hladík, Lukáš ; Kvasnica, Lukáš (referee) ; Uhlířová, Hana (advisor)
This bachelor thesis deals with creation of an user computer program for processing of phase contrast images from a digital holographic microscope. The theoretical section of the thesis contains basic information about obtaining and evaluation of processed images, including a description of their digital representation in the computer. The experimental part deals with techniques and algorithms on which the program is built. This part also contains a description of the graphical user interface of the program and evaluate the impact of different user settings for output files properties.
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Correction of phase image background in the digital holographic microscope using convolution
Rudolfová, Zdena ; Malina, Radomír (referee) ; Uhlířová, Hana (advisor)
This bachelor thesis concentrates on a correction of background in the phase image of cells from a transmitted-light digital holographic microscope (TDHM). Optical aberrations in the optical systems of the object and reference arms cause "deformation" of the phase image. The cell is not displayed on a background with a constant value of phase, it is displayed on a background with phase values continuously changing between different places in the image. A method for removing the consequence of this imperfection from the image is described in this thesis. The principle lies in partial convolution of the phase image with a convolution kernel determined by a two-dimensional Gaussian function with the same variance in the both axes. To eliminate loss of information about the cells, the convolution is computed only from those parts of the phase image which contain no cells. The result of the convolution is considered to be an approximation of the background. This approximation is then subtracted from the phase image. The resulting phase image has a constant background, containing only noise. The necessary mathematical concepts are resumed in the introductory part of the thesis. The basic principle of the TDHM image reconstruction is also described. As a part of the thesis, a computer programme Odečet pozadí (Background subtraction) was created, which processes the phase images from the TDHM using this method.
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