Jobs - Topics of PhD study

Biophysical interpretation of quantitative phase image by means of coherence-controlled holographic microscopy and machine learning

The work will be dealing with the interpretation of the quantitative phase images gained by coherence-controlled holographic microscopy (CCHM). The possibilities for automated analysis of quantitative phase images by means of supervised and unsupervised machine learning will be investigated. The quantitative phase images enable extraction of valuable features characterizing the distribution of dry mass within the cell and hence provide important information about the live cell behaviour. The work would focus on refinement of the present automated classification of cells while employing the quantitative information from both the single-time-point and time-lapse quantitative phase images. The proposed methods will be tested on the images of live cells in order to estimate the applicability in the cancer cell biology.

Supervisor: Chmelík Radim, prof. RNDr., Ph.D.

New methods of control for holographic microscopy

Coherence-controlled holographic microscopy is focused on the observation of living cells in vitro. Long-term observation of living cells necessarily requires automated control of both microscope and experiment. The first goal is to design a new optical arrangement of a fully automated microscope, its mechanical design, and creation of the control software. Another goal is to propose methods for automation of biological experiments, implementing them into control software, and testing in real experiments. Requirements for applicants are optomechanical designer with basic knowledge of robotics.

Supervisor: Chmelík Radim, prof. RNDr., Ph.D.

Complex automated bioreactor for holographic microscopy

For maximum information yield about live cells behaviour provided by coherence controlled holographic microscopy it is inevitable to design and develop complex automated bioreactor. Such a device should ensure optically suitable accommodation of live cells in the microscope with provision of control over physiological microenvironment and preprogrammed challenges. The task is to design, develop and validate the complex automated biorector for T1 holographic microscope.

SupervisorVeselý Pavel, MUDr., CSc.

Polarization multiplexing in correlation and holographic imaging 

Correlation and holographic imaging are techniques that allow either quantitative phase or three-dimensional image reconstruction from interference pattern. The doctoral thesis aims to implement new configurations for correlation and holographic imaging, where the light is multiplexed into orthogonal polarization states rather than divided into independent optical paths. Such systems are expected to improve existing and provide new imaging features, which are unavailable in up-to-date experiments. The required polarization states will be generated and modulated using the electro-optic effect in liquid crystal molecules or new generation optical components working on geometric phase.

Supervisor: Chmelík Radim, prof. RNDr., Ph.D.

Testing putative anti-cancer drugs using Holographic Incoherent Quantitative Phase Imaging (hiQPI)

Perform a screen with a set of putative drugs with potential effect on malignancy, particularly cell motility which is important for invasion and metastasis, with established cell lines derived from common aggressive carcinomas such as A549 (model for Non-Small Cell Lung Cancer). Cell motility will be measured using hiQPI with sub-confluent cell cultures. The project will include microscopy, image processing, data analysis and tissue culture.

SupervisorZicha Daniel, Ing., CSc.

Holographic Incoherent Quantitative Phase Imaging (hiQPI) in biomedical applications

Application of hiQPI for measurements of dynamic dry-mass distributions in live cancer cells in tissue culture including primary cells from patient biopsy. Development of relevant image processing and data analysis for quantitative evaluation of statistically significant changes in cellular responses to chemotherapeutic drugs using dynamic morphometric parameters derived by image processing. The project will include developments in microscopy, image processing, data analysis and tissue culture.

Supervisor: Zicha Daniel, Ing., CSc.

Rigorous simulation of electromagnetic wave propagation in inhomogeneous media 

The topic is focused on development of numerical methods for rigorous simulation of electromagnetic wave propagation in arbitrary inhomogeneous media. Namely, we assume investigation of the techniques based on the expansion into plane waves and/or eigenmodes in combination with perturbation techniques. Developed techniques will applied to modeling of light scattering by selected biological samples. Requirements: knowledge in fields of electrodynamics and optics corresponding to undergraduate courses, basic ability to write computer code, preferably in Matlab.

Supervisor: prof. RNDr. Jiří Petráček, Dr.