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Coherence Controlled Holographic Microscope with the digital optics
Vavřinová, Jana ; Jákl, Petr (referee) ; Dostál, Zbyněk (advisor)
The Digital Micromirror Device (DMD) technology has been developed especially for Digital Light Processing projectors, which allow the image projection. After this succesful implementation, and thanks to the commercial availibility and low initial cost of the DMD chip, a wide range of other applications became possible. Besides, it may be used in microscopy as a spatial light modulator. For example in Coherence-Controlled Holographic Microscope (CCHM) that finds its use especially for imaging and measurement of live-cell dynamic processes. The DMD chip placed in the illumination part of CCHM allows for broadening the application possibilities. Namely it could be different illumination mode experiments or tomographic applications. The master's thesis deals with the optical design of CCHM with digital optics, i. e. DMD chip. The selection of optical elements for CCHM, the experimental verification of the imaging setup and the process of designing the illumination part are described in detail. In the end, the analysis of different designs for illumination setup with the digital optics in object arm is carried out and the results are compared.
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3D printed microscopes
Žáková, Veronika ; Jákl, Petr (referee) ; Dostál, Zbyněk (advisor)
Modular microscope building kits allow those interested in microscopy to get a hands-on introduction to the construction of a light microscope. For this reason, it would be appropriate to equip the laboratories of the Institute of Physical Engineering at Brno University of Technology with such a kit. The inspiration can be found in the open source project openUC2, which offers optical kits based on a combination of 3D printed and commercially available optical components. The aim of my work is to use the open source parts database and supplement it with my own designs that would enable the construction of specialized polarization and fluorescence microscopes. The first part of the thesis introduces light microscopy methods and the equipment that is essential for their proper operation. Next, the 3D printing methods that are applicable to the fabrication of the designed parts are summarized. Beyond the openUC2, the design of a Köhler illuminator, a motorized stage and a motorized objective slider based on commonly available parts are introduced. A transmission microscope, a reflective polarizing microscope and a light sheet microscope were designed based on the UC2 kit with my construction modules. The first two have been assembled and tested along with their control software.
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The adjusting collimator for the Fluorescent holographic microscope
Hlaváčová, Kateřina ; Jákl, Petr (referee) ; Dostál, Zbyněk (advisor)
For the proper function of the Fluorescence olographic microscope, it is necessary to adjust all the optical components of the microscope. Furthermore, the precise adjustment is the very critical condition for proper imaging of the Coherence-controlled holographic microscope. Therefore, it is necessary to create a sight collimator for these microscopes for their adjustment. The fluorescence holographic microscope is based on an interference and holographic principles, whose history is mentioned in the theoretical part of the thesis. The existing state of the art of laser sight collimators and their use in practice is also mentioned. The optical and mechanical design of the laser sight collimator and its realization are described in the next part of the thesis. The software for detecting the black sight cross was created for the use of the laser sight collimator in practice. The software is necessary to evaluate the correctness of the alignment of the adjusted microscope. The descriptions of the adjustment procedures for the laser sight collimator and for the Fluorescence holographic microscope are mentioned in the last part of the thesis. These procedures are necessary for proper manipulation and use with the proposed laser sight collimator.
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Development of Biophysical Interpretation of Quantitative Phase Image Data
Křížová, Aneta ; Jákl, Petr (referee) ; Vomastek, Tomáš (referee) ; Chmelík, Radim (advisor)
This doctoral thesis deals with biophysical interpretation of quantitative phase imaging (QPI) gained with coherence-controlled holographic microscope (CCHM). In the first part methods evaluating information from QPI such as analysis of shape and dynamical characteristics of segmented objects as well as evaluation of the phase information itself are described. In addition, a method of dynamic phase differences (DPD) is designed to allow more detailed monitoring of cell mass translocations. All of these methods are used in biological applications. In an extensive study of various types of cell death, QPI information is compared with flow cytometry data, and preferably a combination of QPI and fluorescence microscopy is used. The DPD method is used to study mass translocations inside the cell during osmotic events. The simplified DPD method is applied to investigate the mechanism of tumor cell movement in collagen gels.
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Computer Generated Holograms
Tvarog, Drahoslav ; Jákl, Petr (referee) ; Kotačka, Libor (advisor)
The presented Diploma thesis deals with the computer-generated diffractive structures or rather called computer generated holograms (CGH). We follow basic principles of classical holography and in the context of which we define a synthetic holography. We then show various types of digital holograms and methods of measurement of their quality. We deal with several iterative algorithms useful for computation of the Fourier transform as well as with methods of phase quantization. In the second part of the work, we describe briefly our computer code for iterative Fourier transform computation. With respect to the mentioned techniques, we further present the usability of the method for design of computer generated holograms in reflection regime. After a short introduction to the electron beam lithography and its exploitation for the origination of computer generated diffractive optical elements. We analyze reconstructions of produced holograms and evaluate its quality.
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Micropositioning tracking system
Svoboda, Tomáš ; Šerý, Mojmír (referee) ; Jákl, Petr (advisor)
This bachelor's thesis deals with the design and construction of a micro positioning device that will monitor the movement of a robotic mouse in a defined space with the help of a camera. The main task will be to assemble a moving platform, the aim of which will be to be in constant contact with the robot below it and to copy its 2D trajectory. The device will then be applied to a live mouse for in vivo holographic endoscopy experiments.
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Controlling and Evaluation of Laser Micromanipulation Experiments
Kaňka, Jan ; Jákl, Petr (referee) ; Provazník, Ivo (advisor)
This work is focused on the development of a user friendly software interface using the LabViewTM environment that simplifies running of various experiments using laser micromanipulations and laser microspectroscopy of living microorganisms. Both techniques have been developing very fast for the last decade and belong to the growing group of contact-less and nondestructive techniques for manipulation and diagnostics of individual living microorganisms, cells, or viruses. Within this project we mastered the driving of peripheries, calibration of CCD scene, real-time image processing of the CCD scene, automatic selection of the cell for further laser processing, acquisition and processing of the Raman spectrum from living microorganisms. The final goal of our activity is fully automatic laser-based sorter of living cells depending on their chemical compositions. This work has been elaborated at the Institute of Scientific Instruments of the ASCR, v.v.i. under the supervision of prof. Pavel Zemanek.
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Correlation and Spiral Microscopy using a Spatial Light Modulation
Bouchal, Petr ; Čižmár,, Tomáš (referee) ; Jákl, Petr (referee) ; Petráček, Jiří (advisor)
Dizertační práce je uceleným shrnutím výsledků dosažených v průběhu doktorského studia. V úvodní části práce je představena motivace, odborné a technické zázemí a grantová podpora realizovaného výzkumu. Popsány jsou také dosažené výsledky a jejich význam pro skupinu Experimentální biofotoniky, Ústavu fyzikálního inženýrství, Vysokého učení technického v Brně. Vědecká část práce je rozdělena do dvou hlavních bloků, které se postupně zabývají návrhem nových zobrazovacích koncepcí a technickou modifikací stávajících zobrazovacích systému v praktických aplikacích. Dosažené vědecké výsledky podporují vývoj v oblastech korelační a spirální mikroskopie s prostorovou modulací světla. V části zabývající se návrhem nových zobrazovacích koncepcí je provedena studie korelačního zobrazení v podmínkách proměnné časové a prostorové koherence. Následně jsou zkoumány možnosti praktického využití vírových a nedifrakčních svazků v oblastech korelační, holografické a optické mikroskopie. Interference vírových svazků a samozobrazení nedifrakčních svazků je postupně využito k dosažení 3D zobrazení s hranovým kontrastem a rotující bodovou rozptylovou funkcí. Pokročilé zobrazovací metody jsou úspěšně zavedeny optickou cestou ale i digitální modifikací holografických záznamů. Výsledky teoretických modelů a numerických simulací jsou doprovázeny praktickým vyhodnocením navržených zobrazovacích principů. V technicky zaměřené části jsou navrženy nové způsoby zavedení prostorové modulace světla, které umožňují rozšíření zorného pole v experimentech korelačního zobrazení a dosažení achromatizace při zobrazení pomocí programovatelných difraktivních prvků. Rozšíření zorného pole v korelačních experimentech umožňuje přizpůsobovací optický systém vložený do standardní zobrazovací sestavy. Achromatizace difraktivního zobrazení je zajištěna použitím speciálně navrženého refraktivního korektoru. V navazující části je navržena nová metoda krokování fáze, která pracuje s dvojlomností kapalných krystalů využívaných v systémech pro prostorovou modulaci světla. Použití metody je experimentálně demonstrováno v polarizačně modifikovaném Mirau interferometru. Získané technické zkušenosti jsou využity v praktickém návrhu a realizaci multimodálního zobrazovacího systému s prostorovou modulací světla.
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