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X-ray computed tomography of mouse embryo
Šejnohová, Marie ; Walek, Petr (referee) ; Kolář, Radim (advisor)
The aim of this semestral thesis is to compare the possibilities of available micro-CT systems. Theoretic part of this thesis there deals with possibilities of staining soft tissues and embryos because of enhancement the contrast of micro-CT images. Here follows a description of sources X-ray and detectors of available micro-CT systems. In practice there was realized the staining of embryo in cooperation with Department of histology and embryology in Brno. Then followed a measuring on FSI in Brno, ČVUT in Prague and synchrotron Elettra in Italy. In semestral thesis are described of the thesis there are compared the micro-CT systems and results of measuring embryos by means of presented systems and results are compared.The best results were obtained on micro-CT in Brno, where X-ray tube and flat panel detector were used. This images were used for a segmentation of cartilage olfactory system by means of 3D region growing. From results they were created 3D models for comparison with a manually segmented model. A less accurate results were obtain with the semi-automatic segmentation but this method isn’t too time-consuming.
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Analysis of methods for evaluation ETICS dirtiness
Krejčík, Jakub ; Žák,, Antonín (referee) ; Žižková, Nikol (advisor)
This diploma thesis deals with problems of dirtiness of surface layers of ETICS (External thermal insulation contact system). In the theoretical part, soil damping agents and processes occurring when adhering dirt are described. The practical part then evaluates the impact of the aspects described below on their dirtyness. At the same time, it monitors the differences in staining depending on the type of material and the manufacturer. A methodology for artificial staining with controllable and repeatable conditions was developed in a special simulator, and this methodology was also verified practically. Simultaneously, individual plasters were exposed to the natural environment, for comparison of laboratory and actual conditions.
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Blood vessel tree segmentation of the mouse liver in CT data
Smékalová, Veronika ; Odstrčilík, Jan (referee) ; Kolář, Radim (advisor)
The methodology of visualization of soft tissue is in biology and medicine a topic for many years. During this period there were approving many techniques how to achieve accurate and authentic image of the researched object or structure. X-ray computed tomography is very helpful to get this goal but is necessary to improve contrasting techniques as well as the techniques of image post-processing. This thesis deals with imaging soft tissue. Specifically, it focuses on mouse liver contrasting with the artificial resin Microfil. Thesis also describes image processing technique (thresholding and region growing) for the data of the measurement with the goal of the visualization of the sample in 3D.
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Segmentation of soft tissues in facial part of mouse embryos from X-ray computed microtomography data
Janštová, Michaela ; Harabiš, Vratislav (referee) ; Chmelík, Jiří (advisor)
This diploma thesis deals with a segmentation of soft tissues in facial part of mouse embryos in Matlab. Segmentation of soft tissues of mouse embryos was not fully automated and every case needs a specific solution. Solving parts of this issues can provide valuable data for evolutionary biologists. Issues about staining and segmentation techniques are described. On the basis of accessible literature otsu thresholding, region growing, k-means clustering and segmentation with atlas were tested. In the end of this paper are those methods tested and evaluated on 3D microtomography data.
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Testing of new methods of animal tissue staining
Feitová, Věra ; Veselá, Mária (referee) ; Klusáková,, Jarmila (advisor)
For accurate diagnosis, detailed information about tissue structure and pathology is often needed. A biopsy is a diagnostic test, used to obtain tissue samples for further examination. The tissue undergoes fixation, cutting, dehydratation, paraffin embedding, slicing, rehydratation and staining. Silver may be used to mark recection borders, when the tissue sample is immersed in a 10% aquous solution of argent nitrate. After cutting, the silver is developed using a commonn black and white photographic developer. Another option is immersing the tissue sample into an aquous solution of ferric chloride and, after cutting, using an aquous solution of potassium ferrocyanide to produce ferric ferrocyanide, otherwise knows as Prussian blue.
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Analysis and optimization of the dyeing process of surgical instruments
Roušarová, Kateřina ; Jugl, Adam (referee) ; Krouská, Jitka (advisor)
This bachelor thesis deals with the issue of staining of disposable surgical instruments in the corporate facility of the industrial partner with whom the cooperation took place. Within the framework of this bachelor thesis an analysis of the input organic raw materials, which are an essential part of the manufactured dye for instrument staining, was carried out. The basic characterization of the raw materials was carried out by available methods at the Faculty of Chemistry, such as density measurement with a hydrometer, viscosity measurement with an automatic viscometer and viscosity versus shear rate with a rheometer. Subsequently, a visual assessment of the behaviour of the individual liquid feedstocks in water was performed. The tabulated values of the raw materials from the safety data sheets were verified by these methods. It was found that the starting ingredients are insoluble in water, in which they precipitate and thus significantly affect the viscosity of the resulting suspension. The actual laboratory preparation of the paint samples was carried out, where 7 samples were mixed, varying in the volumes of the input liquid organic components. These samples were subjected to rheological measurements, which resulted in the dependence of viscosity on shear rate. A range of 0,4–0,8 Pas at a shear rate of 10 s-1 was specified by the industrial partner for the resulting viscosity of the mixed suspension, within which 4 samples fell. The result of the spout test performed using a Ford spout cup determined the time of suspension discharge from the cup, which can be used to verify the quality and correct consistency of the paint mixed in company operation. All samples were stained with surgical instruments and the quality of staining was evaluated after firing. Based on the requirements of the industrial partner, 4 samples were designed falling within the required viscosity range and suitable for staining surgical instruments. The results have been passed on to the industrial partner, who has the discretion to implement new dye preparation procedures in their operation.
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Hafnium Chloride, an Alternative Staining Reagent for Biological Electron Microscopy
BARANYI, Magdalena Victoria
This study focuses on the staining pattern of the non-radioactive heavy metal EM stain HfCl4, used during freeze substitution specimen preparation. HfCl4 was investigated as an alternative for the prominent uranyl acetate, since uranium based materials have been placed under heavy restrictions and bans worldwide. We have found a strong HfCl4 staining pattern of microtubules in myoepithelial cells of Ixodes ricinus salivary glands. Additionally, in several samples, HfCl4 was found to completely fill the cytoplasm of the myoepithelial cells. Nonetheless, artefact formation around granulated cells was also experienced.
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Segmentation of soft tissues in facial part of mouse embryos from X-ray computed microtomography data
Janštová, Michaela ; Harabiš, Vratislav (referee) ; Chmelík, Jiří (advisor)
This diploma thesis deals with a segmentation of soft tissues in facial part of mouse embryos in Matlab. Segmentation of soft tissues of mouse embryos was not fully automated and every case needs a specific solution. Solving parts of this issues can provide valuable data for evolutionary biologists. Issues about staining and segmentation techniques are described. On the basis of accessible literature otsu thresholding, region growing, k-means clustering and segmentation with atlas were tested. In the end of this paper are those methods tested and evaluated on 3D microtomography data.
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Analysis of methods for evaluation ETICS dirtiness
Krejčík, Jakub ; Žák,, Antonín (referee) ; Žižková, Nikol (advisor)
This diploma thesis deals with problems of dirtiness of surface layers of ETICS (External thermal insulation contact system). In the theoretical part, soil damping agents and processes occurring when adhering dirt are described. The practical part then evaluates the impact of the aspects described below on their dirtyness. At the same time, it monitors the differences in staining depending on the type of material and the manufacturer. A methodology for artificial staining with controllable and repeatable conditions was developed in a special simulator, and this methodology was also verified practically. Simultaneously, individual plasters were exposed to the natural environment, for comparison of laboratory and actual conditions.
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Blood vessel tree segmentation of the mouse liver in CT data
Smékalová, Veronika ; Odstrčilík, Jan (referee) ; Kolář, Radim (advisor)
The methodology of visualization of soft tissue is in biology and medicine a topic for many years. During this period there were approving many techniques how to achieve accurate and authentic image of the researched object or structure. X-ray computed tomography is very helpful to get this goal but is necessary to improve contrasting techniques as well as the techniques of image post-processing. This thesis deals with imaging soft tissue. Specifically, it focuses on mouse liver contrasting with the artificial resin Microfil. Thesis also describes image processing technique (thresholding and region growing) for the data of the measurement with the goal of the visualization of the sample in 3D.
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