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Application, analysis and evaluation of a novel medical image annotation and segmentation tools
Sucháček, Jan ; Paštěka, Richard (referee) ; Dr.Benjamin Ramberger, MSc. BSc. BSc. (advisor)
This thesis explores the creation of 3D models of the human upper airways from CT scans to enhance the understanding of complex anatomical details of the upper airways, assist in detecting pathological changes, and facilitate therapeutic decision-making. These models also enable simulation and assessment of airflow characteristics within the human upper airways. To generate these 3D models, two annotation and three segmentation methods were employed on a dataset of six patient CT scans. Various metrics, such as the number of triangles, surface area, volume, model intersection volume, Dice coefficient, and modelto-model distance, were calculated for all resulting 3D models to characterize the models and compare the methods. A detailed analysis focused on four anatomical parts: the nasal cavity with sinuses, pharynx, larynx, and trachea, was performed. Additionally, a computational fluid dynamics (CFD) simulation was conducted on one model to analyze airflow in the upper airways during breathing. This simulation provided insights into airflow dynamics inside the upper airways, potentially reducing the need for invasive examinations. The findings of this thesis demonstrate the potential of 3D upper airway models to improve diagnostic accuracy, treatment planning, and patient outcomes in respiratory medicine.and compare the methods. A detailed analysis focused on four anatomical parts: the nasal cavity with sinuses, pharynx, larynx, and trachea, was performed. Additionally, a computational fluid dynamics (CFD) simulation was conducted on one model to analyze airflow in the upper airways during breathing. This simulation provided insights into airflow dynamics inside the upper airways, potentially reducing the need for invasive examinations. The findings of this thesis demonstrate the potential of 3D upper airway models to improve diagnostic accuracy, treatment planning, and patient outcomes in respiratory medicine.
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Experimental evaluation of medical nebulizers
Zajacová, Lucia ; MSc, Lara Alina Schöllbauer (referee) ; Paštěka, Richard (advisor)
S narastajúcimi problémami v globálnych atmosférických podmienkach stúpa aj výskyt respiračných ochorení a s ním súvisí aj nárast dopytu po efektívnejších zariadeniach na ich liečbu. Medzi takéto zariadenia patrí aj medicínsky nebulizér, ktorý sa často využíva pri inhalačnej terapii. Aj keď bola jeho účinnosť už mnohokrát overená, stále existuje potreba ďalšieho výskumu a vylepšení. Táto práca sa snaží využiť dostupné štúdie a informácie na vytvorenie experimentálneho prostredia na hodnotenie medicínskych nebulizérov. Obsahuje využitie idealizovaného mechanického modelu horných dýchacích ciest Alberta, dýchacieho simulátora xPULM a optického aerosólového spektrometra PALAS Promo 2000 v kombinácii so senzorom Wellas 2200. Následne sa zameriava na návrh spojení medzi týmito komponentmi a plánovanie metód merania pre presnejšie vyhodnotenie. Tieto metódy poskytujú cenné poznatky o charakteristikách aerosólov produkovaných testovanými nebulizérmi. Výsledkom sú mnohé charakteristické parametre, ako je výstup aerosólu z nebulizéra, jeho rýchlosť, zvyškový objem, veľkosť častíc a ich distribúcia. Hodnotenie sa ďalej sústreďuje na usadenie častíc a stanovenie účinnosti nebulizéra pri dodávaní aerosólových častíc do rôznych častí dýchacieho traktu.
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Evaluation of perfusate solution after ex vivo lung perfusion
Dobrovolná, Terezie ; Enghuber, Florian (referee) ; Paštěka, Richard (advisor)
The aim of this master’s thesis is to introduce lung perfusion procedures and determine the parameters that are connected to the state of the lungs after perfusion and during preservation. In the perfusion process and for storing the lung, the phosphate-buffered saline (PBS) solution is used. The work focuses mainly on the parameters that can be measured and evaluated in the perfusate solution during the perfusion and preservation of the lungs such as pH, total dissolved solids, and proteins. These factors can be measured according to several procedures that are based on different principles. The mentioned process has been selected and implemented with regard to availability, feasibility, and appropriateness given. The pH and TDS parameters have been acquired by electrodes. Therefore, sensor calibration is an integral part of the measure ment. The concentration of the proteins was measured with the Bradford assay where it is important to follow the established protocol. Materials for that were present and provided in the Tissue engineering laboratory. Another intention is to assess the state of the lung tissue, meaning how the lungs gradually change their appearance, weight, and mechanical properties over time. The weight is obtained with the calibrated load cell sensor. For this sensor, a platform had to be assembled in order to function correctly and with great accuracy. From the field of mechanical properties of the lungs, the compliance and PV loops have been selected and presented. Five lungs were used for measurement. The appearance of the lungs changed over time and the necrosis was progressing. The lung viability was preserved with the PBS solution with balanced pH. The value of pH was maintained around pH 7. The concentration of the total dis solved solids (TDS) was determined and similar values were obtained in all lungs because the same solution was used. The TDS fluctuated slowly same as pH because they are correlated. The weight of the lungs decreased with passage of the time as expected. Protein concentration increased over time. That can indicate the inflammatory processes in the lung tissue or lung injury. The surface temperature was also obtained with a laser thermometer and decreasing values were noted with increasing storage time. Static compliance had unexpected charac teristics in some of the lungs. This was probably influenced by leakage due to an unsecured trachea. The last parameter was PV loops. The shape of the PV loops looked good until 48h in the majority of the loops. Then, the shape flatted and the shortage of curves appeared due to shortness of breath.
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Modelling of flow and pressure characteristics in the model of the human upper respiratory tract under varying conditions
Karlíková, Adéla ; Forjan,, Mathias (referee) ; Paštěka, Richard (advisor)
Cílem této diplomové práce je vytvořit 3D model horních dýchacích cest podle originálního modelu segmentovaného z CT dat, aplikovat různé podmínky na průtok vzduchu v modelu, a poté hodnotit změnu charakteristik rychlosti a tlaku. Model horních dýchacích cest byl vytvořen v prostředí softwaru ANSYS, který využívá výpočetní dynamiku tekutin, a byly použity Navier-Stokesovy rovnice pro modelování průtoku vzduchu v modelu. Nejprve byl vytvořen jednoduchý 2D model za účelem seznámení se s prostředím ANSYS. Dále byl zkonstruován 3D model horních dýchacích cest a byly modelovány charakteristiky rychlosti a tlaku za různých podmínek. Tyto podmínky zahrnují různé umístění a množství míst pro odběr vzorků v modelu a výběr různých kombinací vstupů. Nakonec byly prezentovány a hodnoceny výsledky spolu s ilustracemi modelů modelovaných za různých podmínek. 3D model lze považovat ze kompromis mezi výpočetní náročností a složitostí modelu a lze jej použít jako základ pro další výzkum.
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Exploring the Population Characteristics of Direction-Selective Ganglion Cells Across the Retinal Space
Svatoň, Jan ; Paštěka, Richard (referee) ; Jösch, Maximilian (advisor)
V minulém století byl vynaložen značný výzkum na pochopení, jak jsou vizuální informace kódovány neurálními populacemi a jejich obvody. Celkový obraz, který vyplynul z tohoto úsilí, naznačuje, že vizuální informace jsou nejprve zpracovány složitými obvody v sítnici a následně přeneseny do vyšších mozkových struktur. Ukazuje se, že sítnice i mozek si vyvinuly pozoruhodně sofistikované výpočty pro extrakci těchto informací. Funkční studie těchto neuronálních transformací byly prováděny pomocí elektrofyziologických nebo zobrazovacích technik. Tyto techniky omezovaly analýzu prostorových specializací sítnice, a to buď počtem dostupných elektrod (v elektrofyziologii) nebo velikostí zorného pole (FOV) (v zobrazovacích experimentech). Pro ukázku – záznamy aktivit gangliových buněk sítnice (RGC) byly omezeny na relativně malou oblast (~ 200 x 200 um2) za použití nejmodernějších zobrazovacích technik. Ve své diplomové práci jsem prozkoumal nově vyvinutou metodu využívající FOV, která je 40krát větší ve srovnání s FOV konvenčních optických metod, což mi umožňilo překonat toto technické omezení. Práce využívá tuto novou zobrazovací metodu k prozkoumání populačních charakteristik směrově selektivních gangliových buněk (DSGC) v sítnicích myší. Replikací již známých populačních vzorců jsme verifikovali, že naše nová zobrazovácí metoda funguje. Práce dále zkoumá účinky pomocných látek pro zvýšení míry infekce RGCs. Tyto pomocné látky tak mohou potenciálně usnadnit nezaujaté zaznamenávání aktivit RGCs. Práce navíc představuje nový stimul pro inspekci receptivních polí (RF) RGCs. Tento nový stimul překonává konvenční stimuly používané v současných studiích jak v rozlišení vyprodukovaného RF, tak v nezbytném čase prezentace stimulu a otevírá tak dveře pro následující studie, které mohou poprvé popsat distribuční vzorce receptivních poli napříč sítnicí a zlepšit tak klasifikaci buněčných tříd.
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Development of an ex vivo lung perfusion system focusing on the preservation of fresh animal lungs for experiments and storage
Mesíková, Klaudia ; Forjan, Mathias (referee) ; Paštěka, Richard (advisor)
A mechanical combined lung model is a type of model used in human breathing simulation. The biggest currency of the model is a high similarity with the human lungs. In order to work with the animal lungs for a longer time and so follow the principles of the 3Rs, a perfusion system is involved in the procedure. The perfusion system filled with a chosen perfusate solution is responsible to prolong the period in which the animal lungs are viable for experiments and storage in the ex-vivo environment. The development of the properly functioning perfusion system is based on the several components included in the process. Choosing the right solution for the perfusion of the inner environment of the lungs is one of the most important things that need to be taken into account. The roller pump is considered the drive motor of the system. Pressure and flow sensors are responsible for monitoring the process parameters that could describe the functionality and the ability to preserve the animal lungs in the ex-vivo environment. The validation of the developed system by using the fresh animal lungs is a part of the thesis as well as the checking procedure of the solution’s influence with the time of the storage. The perfusion system was successfully created and tested. The pressure and flow parameters gained during the measurement were compared while using the saline solution, the Ringer’s solution, and Histofix in the system. The compliance parameter of the lungs were been monitored during the perfusion as well as during the storage with the aim to determine the behaviour of the preserved lungs with the time and the impact of the chosen solution on it. Compliance initially decreased and then stabilized at a certain value throughout the storage period. For the perfusion with the saline and Ringer’s solution, it dropped by one-third. For Histofix preservation, the drop was by half of the initial compliance. The preservation time without the presence of the tissue necrosis was 120 hours using the Saline solution, 240 hours using the Ringer’s solution, and at least 268 hours using Histofix. The perfusion system could further be used in medical research and make a positive aspect in terms of less consumption of the animal organs for experimental purposes in various fields of the research. For future research, the improvement of the perfusion system and solution composition to ensure even longer preservation is welcomed.
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Oscilloscope with the Android Operating System
Paštěka, Richard ; Balogh, Jaroslav (referee) ; Sekora, Jiří (advisor)
Bachelor thesis deals with the design of digital oscilloscope using the Arduino development kit. The theoretical part of the thesis discusses the basic parameters of digital oscilloscopes, sampling types and general characteristics of A/D converters. The thesis further focuses on the description of the development platform Arduino Mega ADK. The practical part describes the steps in the implementation of the oscilloscope. The general design transfers to a specific description of software and hardware solutions. The software consists of two mutually communicating programs. First, program of the microcontroller performs data acquisition. The second is used to render the measured waveforms on the computer screen. Hardware appropriately adjusts the measuring signal for measurement purposes befor Arduino Mega ADK platform. In the results the evaluation of the created oscilloscope waveforms and parameters is given tested by using a function generator.
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Integration and testing of a real time processing unit for lung simulation
Paštěka, Richard ; Drauschke, Andreas (referee) ; Sekora, Jiří (advisor)
Aktivní mechanický plicní simulátor (iLung) nabízí možnost simulace lidského dýchání. Cílem této práce je implementovat a otestovat řídící a akviziční systém cRIO pracující v reálném čase, jako řídící jednotku simulátoru. Výsledné propojení obou zařízení je zdokumentováno ve formě tabulek a původních osazovacích výkresů, které jsou doplněny o popis funkce každého pinu. Významného zlepšení bylo dosaženo laděním motoru a modifikací proporcionálně-integračního regulátoru v řídícím programu. Tyto modifikace mají za následek významné snížení oscilací v okolí nuly. Pro zvýšení využitelnosti a přístupnosti simulátoru byl vytvořen uživatelský manuál a s ním související laboratorní cvičení. Validace funkce implementované řídící jednotky nebyla omezena pouze na jednoduché testovací rutiny, ale rozšířena na testování funkce simulátoru jako celku. Měření na simulátoru byly porovnány a diskutovány s klidovým spirometrickým vyšetřením 20ti probandů. Měření prokázala velkou míru podobnosti mezi simulovaný dýcháním iLung a klidovým lidským dýcháním.
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Evaluation of selected thermophysiological model for the isolated, confined mission in Antarctica
Bečička, Martin ; Dobrovolná,, Julie (referee) ; Paštěka, Richard (advisor)
Over the past few decades, numerous models have been created to estimate human thermal responses. These models rely on energy balance equations that consider the heat exchange between the human body and its environment. These models have substantially progressed from one-node models into complex structures organized in multiple layers and connected by a circulatory blood flow. Although there is literature available comparing the possible utility of the thermophysiological models in different scenarios, little is known about the utility of these mod els in specific conditions. This work investigates and compares selected thermophysiological models, focusing on selecting a suitable model for the use case scenario of Antarctica. The data was collected during a longitudinal study located at Johann Gregor Mendel Czech Antarctic station. The local skin temperature of participants (n = 16) was measured 6 times over the period of the study. The first of each measurement set consisted of orthostatic tests in addition to psychomotor vigilance task and Iowa gambling test present which were present in each of the subsequent measurements. After examining specific experimental conditions, four thermophysiological models were com pared, and the JOS-3 model was determined to be the most appropriate for the thermal data obtained during the experiment. The results revealed that the selected JOS-3 model can accurately predict mean skin temper atures for both experiment designs (RMSD 0.72 and 0.75 C for experiment design 1 and 2 respectively). Furthermore, the JOS-3 model was able to reliably predict head (RMSD 0.82 and 1.13 C), neck (RMSD 0.61 and 1 C), and chest (RMSD 1.01 and 1.22 C) skin temperatures. However, deviations observed for back, hand, and foot segments were significant (RMSD 2.08 - 2.25 and 2.55 - 2.68 C). Possible explanations include uncertainty in clothing insulation of the worn clothing, uncertainty in measurement circumstances (contact with surfaces - floor, table), and the placement of the thermal sensors. The highest deviation was observed in the pelvis (RMSD 2.25 and 3.72 C) and is possibly a result of the JOS-3 model overestimation of heat production in the segment. The study has underscored the significance of obtaining compre hensive data on clothing type and sensor placement for enhancing the accuracy of simulation outcomes.
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Evaluation of perfusate solution after ex vivo lung perfusion
Dobrovolná, Terezie ; Enghuber, Florian (referee) ; Paštěka, Richard (advisor)
The aim of this master’s thesis is to introduce lung perfusion procedures and determine the parameters that are connected to the state of the lungs after perfusion and during preservation. In the perfusion process and for storing the lung, the phosphate-buffered saline (PBS) solution is used. The work focuses mainly on the parameters that can be measured and evaluated in the perfusate solution during the perfusion and preservation of the lungs such as pH, total dissolved solids, and proteins. These factors can be measured according to several procedures that are based on different principles. The mentioned process has been selected and implemented with regard to availability, feasibility, and appropriateness given. The pH and TDS parameters have been acquired by electrodes. Therefore, sensor calibration is an integral part of the measure ment. The concentration of the proteins was measured with the Bradford assay where it is important to follow the established protocol. Materials for that were present and provided in the Tissue engineering laboratory. Another intention is to assess the state of the lung tissue, meaning how the lungs gradually change their appearance, weight, and mechanical properties over time. The weight is obtained with the calibrated load cell sensor. For this sensor, a platform had to be assembled in order to function correctly and with great accuracy. From the field of mechanical properties of the lungs, the compliance and PV loops have been selected and presented. Five lungs were used for measurement. The appearance of the lungs changed over time and the necrosis was progressing. The lung viability was preserved with the PBS solution with balanced pH. The value of pH was maintained around pH 7. The concentration of the total dis solved solids (TDS) was determined and similar values were obtained in all lungs because the same solution was used. The TDS fluctuated slowly same as pH because they are correlated. The weight of the lungs decreased with passage of the time as expected. Protein concentration increased over time. That can indicate the inflammatory processes in the lung tissue or lung injury. The surface temperature was also obtained with a laser thermometer and decreasing values were noted with increasing storage time. Static compliance had unexpected charac teristics in some of the lungs. This was probably influenced by leakage due to an unsecured trachea. The last parameter was PV loops. The shape of the PV loops looked good until 48h in the majority of the loops. Then, the shape flatted and the shortage of curves appeared due to shortness of breath.
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