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Raudenska M, Vicar T, Gumulec J, Masarik M. Johann Gregor Mendel: the victory of statistics over human imagination. Eur J Hum Genet 2023; 31:744-748. [PMID: 36755104 PMCID: PMC9909140 DOI: 10.1038/s41431-023-01303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/11/2023] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
In 2022, we celebrated 200 years since the birth of Johann Gregor Mendel. Although his contributions to science went unrecognized during his lifetime, Mendel not only described the principles of monogenic inheritance but also pioneered the modern way of doing science based on precise experimental data acquisition and evaluation. Novel statistical and algorithmic approaches are now at the center of scientific work, showing that work that is considered marginal in one era can become a mainstream research approach in the next era. The onset of data-driven science caused a shift from hypothesis-testing to hypothesis-generating approaches in science. Mendel is remembered here as a promoter of this approach, and the benefits of big data and statistical approaches are discussed.
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Affiliation(s)
- Martina Raudenska
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Tomas Vicar
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Michal Masarik
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic.
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic.
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, CZ-252 50, Vestec, Czech Republic.
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Kolar R, Vicar T, Chmelik J, Jakubicek R, Odstrcilik J, Valterova E, Nohel M, Skorkovska K, Tornow RP. Assessment of retinal vein pulsation through video-ophthalmoscopy and simultaneous biosignals acquisition. Biomed Opt Express 2023; 14:2645-2657. [PMID: 37342721 PMCID: PMC10278619 DOI: 10.1364/boe.486052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 06/23/2023]
Abstract
The phenomenon of retinal vein pulsation is still not a deeply understood topic in retinal hemodynamics. In this paper, we present a novel hardware solution for recording retinal video sequences and physiological signals using synchronized acquisition, we apply the photoplethysmographic principle for the semi-automatic processing of retinal video sequences and we analyse the timing of the vein collapse within the cardiac cycle using of an electrocardiographic signal (ECG). We measured the left eyes of healthy subjects and determined the phases of vein collapse within the cardiac cycle using a principle of photoplethysmography and a semi-automatic image processing approach. We found that the time to vein collapse (Tvc) is between 60 ms and 220 ms after the R-wave of the ECG signal, which corresponds to 6% to 28% of the cardiac cycle. We found no correlation between Tvc and the duration of the cardiac cycle and only a weak correlation between Tvc and age (0.37, p = 0.20), and Tvc and systolic blood pressure (-0.33, p = 0.25). The Tvc values are comparable to those of previously published papers and can contribute to the studies that analyze vein pulsations.
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Affiliation(s)
- Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Jiri Chmelik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Roman Jakubicek
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Jan Odstrcilik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Eva Valterova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Michal Nohel
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Karolina Skorkovska
- Deparment of Ophthalmology and Optometry, St. Ann University Hospital, Brno, Czech Republic
- Department of Ophthalmology and Optometry, Masaryk University, Brno, Czech Republic
| | - Ralf P. Tornow
- Department of Ophthalmology, Friedrich-Alexander-University Erlangen–Nürnberg, Erlangen, Germany
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Hanelova K, Raudenska M, Kratochvilova M, Navratil J, Vicar T, Bugajova M, Gumulec J, Masarik M, Balvan J. Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles. Cell Commun Signal 2023; 21:120. [PMID: 37226246 DOI: 10.1186/s12964-023-01126-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/06/2023] [Indexed: 05/26/2023] Open
Abstract
Extracellular vesicles (EVs) are important mediators of intercellular communication in the tumour microenvironment. Many studies suggest that cancer cells release higher amounts of EVs exposing phosphatidylserine (PS) at the surface. There are lots of interconnections between EVs biogenesis and autophagy machinery. Modulation of autophagy can probably affect not only the quantity of EVs but also their content, which can deeply influence the resulting pro-tumourigenic or anticancer effect of autophagy modulators. In this study, we found that autophagy modulators autophinib, CPD18, EACC, bafilomycin A1 (BAFA1), 3-hydroxychloroquine (HCQ), rapamycin, NVP-BEZ235, Torin1, and starvation significantly alter the composition of the protein content of phosphatidylserine-positive EVs (PS-EVs) produced by cancer cells. The greatest impact had HCQ, BAFA1, CPD18, and starvation. The most abundant proteins in PS-EVs were proteins typical for extracellular exosomes, cytosol, cytoplasm, and cell surface involved in cell adhesion and angiogenesis. PS-EVs protein content involved mitochondrial proteins and signalling molecules such as SQSTM1 and TGFβ1 pro-protein. Interestingly, PS-EVs contained no commonly determined cytokines, such as IL-6, IL-8, GRO-α, MCP-1, RANTES, and GM-CSF, which indicates that secretion of these cytokines is not predominantly mediated through PS-EVs. Nevertheless, the altered protein content of PS-EVs can still participate in the modulation of the fibroblast metabolism and phenotype as p21 was accumulated in fibroblasts influenced by EVs derived from CPD18-treated FaDu cells. The altered protein content of PS-EVs (data are available via ProteomeXchange with identifier PXD037164) also provides information about the cellular compartments and processes that are affected by the applied autophagy modulators. Video Abstract.
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Affiliation(s)
- Klara Hanelova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martina Raudenska
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Monika Kratochvilova
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jiri Navratil
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Tomas Vicar
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, Czech Republic
| | - Maria Bugajova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Michal Masarik
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- First Faculty of Medicine, Charles University, Katerinska 32, 12108, Prague, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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Raudenska M, Kratochvilova M, Vicar T, Gumulec J, Balvan J, Polanska H, Pribyl J, Masarik M. Author Correction: Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation. Sci Rep 2022; 12:18711. [PMCID: PMC9636195 DOI: 10.1038/s41598-022-23540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Martina Raudenska
- grid.10267.320000 0001 2194 0956Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Monika Kratochvilova
- grid.10267.320000 0001 2194 0956Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomas Vicar
- grid.10267.320000 0001 2194 0956Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, 616 00 Brno, Czech Republic
| | - Jaromir Gumulec
- grid.10267.320000 0001 2194 0956Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.4994.00000 0001 0118 0988Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, 616 00 Brno, Czech Republic
| | - Jan Balvan
- grid.10267.320000 0001 2194 0956Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.4994.00000 0001 0118 0988Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, 616 00 Brno, Czech Republic
| | - Hana Polanska
- grid.10267.320000 0001 2194 0956Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Pribyl
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Masarik
- grid.10267.320000 0001 2194 0956Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.4994.00000 0001 0118 0988Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, 616 00 Brno, Czech Republic
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5
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Fialova JL, Hönigova K, Raudenska M, Miksatkova L, Zobalova R, Navratil J, Šmigová J, Moturu TR, Vicar T, Balvan J, Vesela K, Abramenko N, Kejik Z, Kaplanek R, Gumulec J, Rosel D, Martasek P, Brábek J, Jakubek M, Neuzil J, Masarik M. Pentamethinium salts suppress key metastatic processes by regulating mitochondrial function and inhibiting dihydroorotate dehydrogenase respiration. Biomed Pharmacother 2022; 154:113582. [DOI: 10.1016/j.biopha.2022.113582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022] Open
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Kolar R, Vicar T, Odstrcilik J, Valterova E, Skorkovska K, Kralik M, Tornow RP. Multispectral retinal video-ophthalmoscope with fiber optic illumination. J Biophotonics 2022; 15:e202200094. [PMID: 35604408 DOI: 10.1002/jbio.202200094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Multispectral imaging is used in various applications including astronomy, industry and agriculture. In retinal imaging, the single-shot multispectral image stack is typically acquired and analyzed. This multispectral analysis can provide information on various structural or metabolic properties. This paper describes the multispectral improvement of a video-ophthalmoscope, which can acquire retinal video sequences of the optic nerve head and peripapillary area using various spectral light illumination. The description of the multispectral video imaging is provided and several applications are described. These applications include multispectral retinal photoplethysmography, visualization of spontaneous vein pulsation and multispectral RGB image generation.
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Affiliation(s)
- Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Jan Odstrcilik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Eva Valterova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Karolina Skorkovska
- Department of Ophthalmology and Optometry, St. Ann University Hospital, Brno, Czech Republic
- Department of Ophthalmology and Optometry, Masaryk University, Brno, Czech Republic
| | - Martin Kralik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Ralf-Peter Tornow
- Department of Ophthalmology, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
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Vicar T, Chmelik J, Navratil J, Kolar R, Chmelikova L, Cmiel V, Jagos J, Provaznik I, Masarik M, Gumulec J. Cancer Cells Viscoelasticity Measurement by Quantitative Phase and Flow Stress Induction. Biophys J 2022; 121:1632-1642. [PMID: 35390297 PMCID: PMC9117928 DOI: 10.1016/j.bpj.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/02/2022] Open
Abstract
Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotypisation are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative Phase Imaging (QPI) is used for image acquisition because this technique enables to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live cell experiments and even through a time-lapse, where we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters like circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, where an increase of stiffness corresponded to actin repolymerisation in time.
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Affiliation(s)
- Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic; Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
| | - Jiri Chmelik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic
| | - Jiri Navratil
- Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
| | - Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic
| | - Larisa Chmelikova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic
| | - Vratislav Cmiel
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic
| | - Jiri Jagos
- Dept. of Tissue Biomechanics and Numerical Modelling in Medicine, Faculty of Mechanical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communications, Brno University of Technology, Brno, Czech Republic
| | - Michal Masarik
- Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Masaryk University, Brno, Czech Republic.
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Vicar T, Gumulec J, Kolar R, Kopecna O, Pagacova E, Falkova I, Falk M. DeepFoci: Deep learning-based algorithm for fast automatic analysis of DNA double-strand break ionizing radiation-induced foci. Comput Struct Biotechnol J 2022; 19:6465-6480. [PMID: 34976305 PMCID: PMC8668444 DOI: 10.1016/j.csbj.2021.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 11/26/2022] Open
Abstract
DNA double-strand breaks (DSBs), marked by ionizing radiation-induced (repair) foci (IRIFs), are the most serious DNA lesions and are dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold-standard method in radiation biodosimetry and allows research on DSB induction and repair at the molecular and single-cell levels. In this study, we introduce DeepFoci - a deep learning-based fully automatic method for IRIF counting and morphometric analysis. DeepFoci is designed to work with 3D multichannel data (trained for 53BP1 and γH2AX) and uses U-Net for nucleus segmentation and IRIF detection, together with maximally stable extremal region-based IRIF segmentation. The proposed method was trained and tested on challenging datasets consisting of mixtures of nonirradiated and irradiated cells of different types and IRIF characteristics - permanent cell lines (NHDFs, U-87) and primary cell cultures prepared from tumors and adjacent normal tissues of head and neck cancer patients. The cells were dosed with 0.5-8 Gy γ-rays and fixed at multiple (0-24 h) postirradiation times. Under all circumstances, DeepFoci quantified the number of IRIFs with the highest accuracy among current advanced algorithms. Moreover, while the detection error of DeepFoci remained comparable to the variability between two experienced experts, the software maintained its sensitivity and fidelity across dramatically different IRIF counts per nucleus. In addition, information was extracted on IRIF 3D morphometric features and repair protein colocalization within IRIFs. This approach allowed multiparameter IRIF categorization of single- or multichannel data, thereby refining the analysis of DSB repair processes and classification of patient tumors, with the potential to identify specific cell subclones. The developed software improves IRIF quantification for various practical applications (radiotherapy monitoring, biodosimetry, etc.) and opens the door to advanced DSB focus analysis and, in turn, a better understanding of (radiation-induced) DNA damage and repair.
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Key Words
- 53BP1, P53-binding protein 1
- Biodosimetry
- CNN, convolutional neural network
- Confocal Microscopy
- Convolutional Neural Network
- DNA Damage and Repair
- DSB, DNA double-strand break
- Deep Learning
- FOV, field of view
- GUI, graphical user interface
- IRIF, ionizing radiation-induced (repair) foci
- Image Analysis
- Ionizing Radiation-Induced Foci (IRIFs)
- MSER, maximally stable extremal region (algorithm)
- Morphometry
- NHDFs, normal human dermal fibroblasts
- RAD51, DNA repair protein RAD51 homolog 1
- U-87, U-87 glioblastoma cell line
- γH2AX, histone H2AX phosphorylated at serine 139
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Affiliation(s)
- Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, Czech Republic.,Czech Academy of Sciences, Institute of Biophysics, v.v.i, Department of Cell Biology and Radiobiology, Kralovopolska 135, Brno, Czech Republic.,Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, Czech Republic
| | - Olga Kopecna
- Czech Academy of Sciences, Institute of Biophysics, v.v.i, Department of Cell Biology and Radiobiology, Kralovopolska 135, Brno, Czech Republic
| | - Eva Pagacova
- Czech Academy of Sciences, Institute of Biophysics, v.v.i, Department of Cell Biology and Radiobiology, Kralovopolska 135, Brno, Czech Republic
| | - Iva Falkova
- Czech Academy of Sciences, Institute of Biophysics, v.v.i, Department of Cell Biology and Radiobiology, Kralovopolska 135, Brno, Czech Republic
| | - Martin Falk
- Czech Academy of Sciences, Institute of Biophysics, v.v.i, Department of Cell Biology and Radiobiology, Kralovopolska 135, Brno, Czech Republic
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Kolar R, Chmelikova L, Vicar T, Provaznik I. Increasing the Image Contrast via Fast Fluorescence Photobleaching. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:2741-2744. [PMID: 34891817 DOI: 10.1109/embc46164.2021.9630859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper focuses on the analysis of image sequences acquired during fast photobleaching using a standard wide-field microscope. We show that the photobleaching rate estimated for each pixel is not constant for the whole field of view, but it provides a new spatially variant parametric image related to the cell structure and diffusion of fluorophores. We also provide an alternative way to estimate a pixel-wise photobleaching rate with significantly less computation time than exponential model fitting.Clinical Relevance- This method provides an additional way how fluorescence photobleaching might be used for increasing the image contrast.
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10
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Vicar T, Gumulec J, Kolar R, Chmelik J, Navratil J, Chmelikova L, Cmiel V, Provaznik I, Masarik M. Parametric Deconvolution for Cancer Cells Viscoelasticity Measurements from Quantitative Phase Images. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:439-442. [PMID: 34891327 DOI: 10.1109/embc46164.2021.9630524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this contribution, we focused on optimising a dynamic flow-based shear stress system to achieve a reliable platform for cell shear modulus (stiffness) and viscosity assessment using quantitative phase imaging. The estimation of cell viscoelastic properties is influenced by distortion of the shear stress waveform, which is caused by the properties of the flow system components (i.e., syringe, flow chamber and tubing). We observed that these components have a significant influence on the measured cell viscoelastic characteristics. To suppress this effect, we applied a correction method utilizing parametric deconvolution of the flow system's optimized impulse response. Achieved results were compared with the direct fitting of the Kelvin-Voigt viscoelastic model and the basic steady-state model. The results showed that our novel parametric deconvolution approach is more robust and provides a more reliable estimation of viscosity with respect to changes in the syringe's compliance compared to Kelvin-Voigt model.
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Vicar T, Chmelik J, Jakubicek R, Chmelikova L, Gumulec J, Balvan J, Provaznik I, Kolar R. Self-supervised pretraining for transferable quantitative phase image cell segmentation. Biomed Opt Express 2021; 12:6514-6528. [PMID: 34745753 PMCID: PMC8547997 DOI: 10.1364/boe.433212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/03/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
In this paper, a novel U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-processing step. Additionally, we proposed a self-supervised pretraining technique using nonlabelled data, which is trained to reconstruct multiple image distortions and improved the segmentation performance from 0.67 to 0.70 of object-wise intersection over union. Moreover, we publish a new dataset of manually labelled images suitable for this task together with the unlabelled data for self-supervised pretraining.
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Affiliation(s)
- Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Chmelik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Roman Jakubicek
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Larisa Chmelikova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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Chmelik J, Jakubicek R, Vicar T, Walek P, Ourednicek P, Jan J. Iterative machine learning based rotational alignment of brain 3D CT data. Annu Int Conf IEEE Eng Med Biol Soc 2020; 2019:4404-4408. [PMID: 31946843 DOI: 10.1109/embc.2019.8857858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The optimal rotational alignment of brain Computed Tomography (CT) images to a required standard position has a crucial importance for both automatic and manual diagnostic analysis. In this contribution, we present a novel two-step iterative approach for the automatic 3D rotational alignment of brain CT data. The angles of axial and coronal rotations are determined by an unsupervised by localisation of the Midsagittal Plane (MSP) method. This includes detection and pairing of medially symmetrical feature points. The sagittal rotation angle is subsequently estimated by regression convolutional neural network (CNN). The proposed methodology has been evaluated on a dataset of CT data manually aligned by radiologists. It has been shown that the algorithm achieved the low error of estimated rotations (≈1 degree) and in a significantly shorter time than the experts (≈2 minutes per case).
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Vicar T, Balvan J, Jaros J, Jug F, Kolar R, Masarik M, Gumulec J. Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison. BMC Bioinformatics 2019; 20:360. [PMID: 31253078 PMCID: PMC6599268 DOI: 10.1186/s12859-019-2880-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast artifacts making automatic segmentation challenging. The aim of this study was to compare the segmentation efficacy of published steps of segmentation work-flow (image reconstruction, foreground segmentation, cell detection (seed-point extraction) and cell (instance) segmentation) on a dataset of the same cells from multiple contrast microscopic modalities. RESULTS We built a collection of routines aimed at image segmentation of viable adherent cells grown on the culture dish acquired by phase contrast, differential interference contrast, Hoffman modulation contrast and quantitative phase imaging, and we performed a comprehensive comparison of available segmentation methods applicable for label-free data. We demonstrated that it is crucial to perform the image reconstruction step, enabling the use of segmentation methods originally not applicable on label-free images. Further we compared foreground segmentation methods (thresholding, feature-extraction, level-set, graph-cut, learning-based), seed-point extraction methods (Laplacian of Gaussians, radial symmetry and distance transform, iterative radial voting, maximally stable extremal region and learning-based) and single cell segmentation methods. We validated suitable set of methods for each microscopy modality and published them online. CONCLUSIONS We demonstrate that image reconstruction step allows the use of segmentation methods not originally intended for label-free imaging. In addition to the comprehensive comparison of methods, raw and reconstructed annotated data and Matlab codes are provided.
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Affiliation(s)
- Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic.,Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic
| | - Josef Jaros
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 664/53, Brno, CZ-65691, Czech Republic
| | - Florian Jug
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden, DE-01307, Germany
| | - Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, Brno, CZ-61600, Czech Republic
| | - Michal Masarik
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic
| | - Jaromir Gumulec
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. .,Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic. .,Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, Brno, CZ-612 00, Czech Republic.
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Raudenska M, Kratochvilova M, Vicar T, Gumulec J, Balvan J, Polanska H, Pribyl J, Masarik M. Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation. Sci Rep 2019; 9:1660. [PMID: 30733487 PMCID: PMC6367361 DOI: 10.1038/s41598-018-38199-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
We focused on the biomechanical and morphological characteristics of prostate cancer cells and their changes resulting from the effect of docetaxel, cisplatin, and long-term zinc supplementation. Cell population surviving the treatment was characterized as follows: cell stiffness was assessed by atomic force microscopy, cell motility and invasion capacity were determined by colony forming assay, wound healing assay, coherence-controlled holographic microscopy, and real-time cell analysis. Cells of metastatic origin exhibited lower height than cells derived from the primary tumour. Cell dry mass and CAV1 gene expression followed similar trends as cell stiffness. Docetaxel- and cisplatin-surviving cells had higher stiffness, and decreased motility and invasive potential as compared to non-treated cells. This effect was not observed in zinc(II)-treated cells. We presume that cell stiffness changes may represent an important overlooked effect of cisplatin-based anti-cancer drugs. Atomic force microscopy and confocal microscopy data images used in our study are available for download in the Zenodo repository ( https://zenodo.org/ , Digital Object Identifiers:10.5281/zenodo.1494935).
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Affiliation(s)
- Martina Raudenska
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Monika Kratochvilova
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Tomas Vicar
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 3058/10, CZ-616 00, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00, Brno, Czech Republic
| | - Jan Balvan
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00, Brno, Czech Republic
| | - Hana Polanska
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Jan Pribyl
- Central European Institute of Technology, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Michal Masarik
- Department of Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic.
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University/Kamenice 5, CZ-625 00, Brno, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00, Brno, Czech Republic.
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