Module for Electrodermal Activity recording

Tato práce popisuje elektrodermální aktivitu (EDA) a její vznik na základě vlastností kůže a termoregulace organismu. EDA je signál mající úzký vztah k psychofyziologii a můžeme jeho pomocí vyhodnocovat nejrůznější emoční, motorické a pozornostní vlivy na lidský organismus. Práce dále rozebírá možnosti snímání kožního potenciálu a vodivosti a popisuje konstrukci zařízení schopného tyto signály měřit a ukládat v počítači.This thesis describes electrodermal activity (EDA) and its origin based on the properties of the skin and thermoregulation of body. EDA is a signal having a close relationship to psychophysiology and its help we can evaluate a variety of emotional, motoric and attentional effects on the human organism. The thesis also discusses the possibility of sensing skin potential and conductatce and how to construct a module for its scanning and uploading to computer.

Cell tracking in images from holographic microscope

Tato práce se věnuje sledování buněk v obrazových sekvencích pořízených pomocí multimodálního holografického mikroskopu (MHM). Princip holografického mikroskopu je zde popsán společně s jeho aplikací pro záznam buněk. Hlavní část práce popisuje společný přístup pro segmentaci a sledování jednotlivých buněk v dlouhodobých záznamech. Navržený přístup je založen na modelu parametrických aktivních kontur se specifickými modifikacemi pro dosažení přiměřené přesnosti a robustnosti. Implementovaná metoda je zde detailně popsána včetně vyhodnocení a ukázky výsledků.This thesis focuses on cell tracking in image sequences acquired using a multimodal holographic microscope (MHM). The principles of holographic microscopy are described together with the application in cells acquisition. The main part of the thesis describes a complete approach for segmentation and tracking of single cells in acquired in long-term sequences. The approach is designed based on parametric active contour models with specific modifications to achieve reasonable precision and robustness. The implemented method is described in detail, including the evaluation and demonstration of results.

Design of a spatial database of standardized blocks of flats for the purpose of population sheltering in the town of Uherské Hradiště

This article describes the process of creating a database of standardized blocks of flats in the territory of the town of Uherské Hradiště. From the perspective of municipalities, one of the issues in the field of sheltering is the lack of a systematic approach unified for all municipalities in the CR. That is why there is ample space for standardization. This is main problem of sheltering in the CR. The design and creation of a database containing buildings suitable as improvised shelters in Uherské Hradiště is the aim of research in this paper. The methods of analysis and synthesis of obtained data were used in the research. For the creation of the spatial database MS Excel was used for the initial outline of the database. Subsequently, QGIS version 2.6.0 and QGIS Browser version 2.6.0 were used. The main spatial data were the OpenStreetMap (OSM) dataset. The blocks of flats were categorized in order to facilitate the design and preparation of population sheltering in the town. The categorization is based on the presumption of consistency in the construction of groups of buildings, which can be divided into concrete high-rise blocks of flats and those of brick. The article maps individual blocks of flats in the territory of Uherské Hradiště and inputs them into the database. The final database consists of two types of the residential buildings structures - brick and panel type. Structural type series are identified according to the type of construction of each object. The database of the most widespread structural type series in Uherské Hradiště contains a total of 364 objects, of which 271 objects are OP 1.11., 33 objects are G32 and 15 objects are OP 1.31. structural type series. The structural type series of 45 objects was not possible to identify. However, 16 objects belong most likely to the brick structure type. The type oneness can be used in the area of population sheltering planning and designing of improvised shelters. The resulting database is then created as a spatial database to support the use of GIS tools. © 2018, World Scientific and Engineering Academy and Society. All rights reserved

Probabilistic Noise2Void: Unsupervised Content-Aware Denoising

Today, Convolutional Neural Networks (CNNs) are the leading method for image denoising. They are traditionally trained on pairs of images, which are often hard to obtain for practical applications. This motivates self-supervised training methods, such as Noise2Void (N2V) that operate on single noisy images. Self-supervised methods are, unfortunately, not competitive with models trained on image pairs. Here, we present Probabilistic Noise2Void (PN2V), a method to train CNNs to predict per-pixel intensity distributions. Combining these with a suitable description of the noise, we obtain a complete probabilistic model for the noisy observations and true signal in every pixel. We evaluate PN2V on publicly available microscopy datasets, under a broad range of noise regimes, and achieve competitive results with respect to supervised state-of-the-art methods

Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison

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

Quantitative Phase Dynamics of Cancer Cell Populations Affected by Blue Light

Increased exposition to blue light may induce many changes in cell behavior and significantly affect the critical characteristics of cells. Here we show that multimodal holographic microscopy (MHM) within advanced image analysis is capable of correctly distinguishing between changes in cell motility, cell dry mass, cell density, and cell death induced by blue light. We focused on the effect of blue light with a wavelength of 485 nm on morphological and dynamical parameters of four cell lines, malignant PC-3, A2780, G361 cell lines, and the benign PNT1A cell line. We used MHM with blue light doses 24 mJ/cm2, 208 mJ/cm2 and two kinds of expositions (500 and 1000 ms) to acquire real-time quantitative phase information about cellular parameters. It has been shown that specific doses of the blue light significantly influence cell motility, cell dry mass and cell density. These changes were often specific for the malignant status of tested cells. Blue light dose 208 mJ/cm2 × 1000 ms affected malignant cell motility but did not change the motility of benign cell line PNT1A. This light dose also significantly decreased proliferation activity in all tested cell lines but was not so deleterious for benign cell line PNT1A as for malignant cells. Light dose 208 mJ/cm2 × 1000 ms oppositely affected cell mass in A2780 and PC-3 cells and induced different types of cell death in A2780 and G361 cell lines. Cells obtained the least damage on lower doses of light with shorter time of exposition

Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles

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 TGF ss 1 pro-protein. Interestingly, PS-EVs contained no commonly determined cytokines, such as IL-6, IL-8, GRO-a, 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