PhD Defence - Jan Dudak

Sep. 9th, 2020 - Sep. 9th, 2020

On September 9, 2020, Ph.D. defense of our colleague, Jan Dudak, took place at the Faculty of Biomedical Engineering at the Czech Technical University in Prague. The topic of the thesis is "Energy Sensitive X-ray radiography and Tomography Optimized for Small Animal Imaging".

This work was carried out under supervision of Stanislav Pospíšil and Jan Jakůbek.


X-ray micro-CT (micro computed tomography), a non-destructive imaging modality providing 3D information on inner structures of an investigated object, has recently become a valuable tool that is widely used in scientific research. The current state-of-the-art laboratory micro-CT systems routinely provide spatial resolution of several micrometers; however, even sub-micron resolution can be nowadays achieved. Small animal X-ray imaging has enabled new approaches of research in biology and pre-clinical field.


Despite the high level of state-of-the-art technologies, several known technology limitations are permanently subjects of continuous development. The conventional X-ray detection technologies suffer from the presence of so called-dark current that reduces the contrast-to-noise ratio of the data and consequently degrades the detectability of fine structures within the data. Furthermore, micro-CT or computed tomography in general, is not capable of quantitative measurements.


This thesis addresses both mentioned drawbacks by utilizing a novel technology of photon-counting detectors for micro-CT imaging. The key advantages of photon-counting technology concerning X-ray imaging are based on dark-current-free operation and energy-resolving capabilities. Dark-current-free photon-counting provides and enhanced contrast of the obtained data, while the energy-resolving capability enables quantitative CT measurements by means of energy-sensitive or so-called spectral radiography and CT.


The thesis focuses on the development of methods and associated equipment for high-resolution and energy sensitive X-ray micro-CT of biological samples using large area photon-counting detectors Timepix. The thesis characterizes the technology of photon-counting detectors and compares it with conventional X-ray imaging cameras. Furthermore, it introduces techniques for data acquisition, processing and hardware accessories developed within the thesis. The key results are based on the applied use of Timepix detectors for micro-CT imaging of diverse biological samples ranging from whole small animals to single-cell organisms. CT measurements with voxel size smaller than 600 nm have been carried out. Important results have been achieved especially in the case of micro-CT of ex vivo soft biology tissue.


The thesis further presents unique results of spectral micro-CT measurements of a phantom object. Experimental results have proven the capability of simultaneous identification and quantification of multiple materials within the scanned object, by using self-implemented four-channel basis material decomposition. Such results achieved using large-area Timepix detectors have not been published so far. The ability of quantitative estimation of content of a target element can potentially open new application areas of CT imaging towards molecular imaging or simultaneous imaging of multiple contrast agents in a single scan.


The thesis statement can be found on the following link.

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