arXiv subjects

Dalibor Stys

Publications and source records attributed to Dalibor Stys.

16 recordsLinked to original sources

arXiv2023

Quantification of collective behaviour via causality analysis

Terms such as leader, mediator, and follower sound equal in the description of a pack of wolves, a street protest crowd, or a business team and have very similar meanings. This indicates the presence of some general law or structure that governs collective behaviour. To reveal this, we selected the most common parameter for most levels of the organisation -- motion. A causality analysis of distance correlations was performed to obtain follow-up networks that show who follows whom and how strongly. These networks characterise an observed system in general and work as an automation bridge between the biological experiment and the broad field of network analysis. The proposed method was tested on 3D image data from a controlled experiment on a 6-member school of aquarium fish of Tiger Barb. The network patterns can be easily ethologically interpreted and agreed with expected behaviour.

q-bio.QM↗

arXiv2022

Cell segmentation from telecentric bright-field transmitted light microscopy images using a Residual Attention U-Net: a case study on HeLa line

Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and microscopy image segmentation tasks due to their success and promising outcomes. The main objective of this paper is to develop a deep learning, U-Net-based method to segment the living cells of the HeLa line in bright-field transmitted light microscopy. To find the most suitable architecture for our datasets, a residual attention U-Net was proposed and compared with an attention and a simple U-Net architecture. The attention mechanism highlights the remarkable features and suppresses activations in the irrelevant image regions. The residual mechanism overcomes with vanishing gradient problem. The Mean-IoU score for our datasets reaches 0.9505, 0.9524, and 0.9530 for the simple, attention, and residual attention U-Net, respectively. The most accurate semantic segmentation results was achieved in the Mean-IoU and Dice metrics by applying the residual and attention mechanisms together. The watershed method applied to this best -- Residual Attention -- semantic segmentation result gave the segmentation with the specific information for each cell.

q-bio.QM↗

arXiv2021

Spectroscopic Approach to Correction and Visualisation of Bright-Field Light Transmission Microscopy Biological Data

The most realistic information about the transparent sample such as a live cell can be obtained only using bright-field light microscopy. At high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872x3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectroscopic approach for the correction of this uncompressed 12-bpc data by simultaneous calibration of all parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8-bpc intensity depth after the Least Information Loss compression.

eess.IV↗

arXiv2021

Estimation of rheological parameters for unstained living cells

In video-records, objects moving in intracellular regions are often hardly detectable and identifiable. In order to squeeze the information on the intracellular flows, we propose an automatic method of reconstruction of intracellular flow velocity fields based only on a recorded video of an unstained cell. The basis of the method is detection of speeded-up robust features (SURF) and assembling them into trajectories. Two components of motion -- direct and Brownian -- are separated by an original method based on minimum covariance estimation. The Brownian component gives a spatially resolved diffusion coefficient. The directed component yields a velocity field, and, after fitting the vorticity equation, estimation of the spatially distributed effective viscosity. The method was applied to videos of a human osteoblast and a hepatocyte. The obtained parameters are in agreement with literature data.

physics.bio-ph↗

arXiv2020

Quasi-spectral characterization of intracellular regions in bright-field light microscopy images

Investigation of cell structure is hardly imaginable without bright-field microscopy. Numerous modifications such as depth-wise scanning or videoenhancement make this method being state-of-the-art. This raises a question what maximal information can be extracted from ordinary (but well acquired) bright-field images in a model-free way. Here we introduce a method of a physically correct extraction of features for each pixel when these features resemble a transparency spectrum. The method is compatible with existent ordinary bright-field microscopes and requires mathematically sophisticated data processing. Unsupervised clustering of the spectra yields reasonable semantic segmentation of unstained living cells without any a priori information about their structures. Despite the lack of reference data (to prove strictly that the proposed feature vectors coincide with transparency), we believe that this method is the right approach to an intracellular (semi)quantitative and qualitative chemical analysis.

eess.IV↗

arXiv2019

Application of electromagnetic centroids to colocalization of fluorescing objects in tissue sections

Light microscopy as well as image acquisition and processing suffer from physical and technical prejudices which preclude a correct interpretation of biological observations which can be reflected in, e.g., medical and pharmacological praxis. Using the examples of a diffracting microbead and fluorescently labelled tissue, this article clarifies some ignored aspects of image build-up in the light microscope and introduce algorithms for maximal extraction of information from the 3D microscopic experiments. We provided a correct set-up of the microscope and we sought a voxel (3D pixel) called an electromagnetic centroid which localizes the information about the object. In diffraction imaging and light emission, this voxel shows a minimal intensity change in two consecutive optical cuts. This approach further enabled us to identify z-stack of a DAPI-stained tissue section where at least one object of a relevant fluorescent marker was in focus. The spatial corrections (overlaps) of the DAPI-labelled region with in-focus autofluorescent regions then enabled us to co-localize these three regions in the optimal way when considering physical laws and information theory. We demonstrate that superresolution down to the Nobelish level can be obtained from commonplace widefield bright-field and fluorescence microscopy and bring new perspectives on co-localization in fluorescent microscopy.

q-bio.QM↗

arXiv2018

Zampa's systems theory: a comprehensive theory of measurement in dynamic systems

The article outlines in memoriam Prof. Pavel Zampa's concepts of system theory which enable to devise a measurement in dynamic systems independently of the particular system behaviour. From the point of view of Zampa's theory, terms like system time, system attributes, system link, system element, input, output, subsystems, and state variables are defined. In Conclusions, Zampa's theory is discussed together with another mathematical approaches of qualitative dynamics known since the 19th century. In Appendices, we present applications of Zampa's technical approach to measurement of complex dynamical (chemical and biological) systems at the Institute of Complex Systems, University of South Bohemia in Ceske Budejovice.

cs.OH↗

arXiv2017

Colorimetric Calibration of a Digital Camera

In this paper, we introduce a novel - physico-chemical - approach for calibration of a digital camera chip. This approach utilizes results of measurement of incident light spectra of calibration films of different levels of gray for construction of calibration curve (number of incident photons vs. image pixel intensity) for each camera pixel. We show spectral characteristics of such corrected digital raw image files (a primary camera signal) and demonstrate their suitability for next image processing and analysis.

cs.CV↗

arXiv2016

Observation of dynamics inside an unlabeled live cell using bright-field photon microscopy: Evaluation of organelles' trajectories

This article presents an algorithm for the evaluation of organelles' movements inside of an unmodified live cell. We used a time-lapse image series obtained using wide-field bright-field photon transmission microscopy as an algorithm input. The benefit of the algorithm is the application of the Rényi information entropy, namely a variable called a point information gain, which enables to highlight the borders of the intracellular organelles and to localize the organelles' centers of mass with the precision of one pixel.

q-bio.QM↗

arXiv2016

Information limits of optical microscopy: application to fluorescently labelled tissue section

The article demonstrates some less known principles of image build-up in diffractive microscopy and their usage in analysis unravelling the smallest localized information about the original object - an electromagnetic centroid. In fluorescence, the electromagnetic centroid is naturally at the position of the fluorophore. The usage of an information-entropic variable - a point divergence gain - is demonstrated for finding the most localized position of the object's representation, generally of the size of a voxel (3D pixel). These spatial pixels can be qualitatively classified and used for reconstruction of the 3D structures with precision comparable with electron microscopy.

physics.med-ph↗

arXiv2016

Super-resolved 3-D imaging of live cells organelles from bright-field photon transmission micrographs

Current biological and medical research is aimed at obtaining a detailed spatiotemporal map of a live cell's interior to describe and predict cell's physiological state. We present here an algorithm for complete 3-D modelling of cellular structures from a z-stack of images obtained using label-free wide-field bright-field light-transmitted microscopy. The method visualizes 3-D objects with a volume equivalent to the area of a camera pixel multiplied by the z-height. The computation is based on finding pixels of unchanged intensities between two consecutive images of an object spread function. These pixels represent strongly light-diffracting, light-absorbing, or light-emitting objects. To accomplish this, variables derived from Rényi entropy are used to suppress camera noise. Using this algorithm, the detection limit of objects is only limited by the technical specifications of the microscope setup--we achieve the detection of objects of the size of one camera pixel. This method allows us to obtain 3-D reconstructions of cells from bright-field microscopy images that are comparable in quality to those from electron microscopy images.

q-bio.QM↗

arXiv2016

Optimal noise in the hodgepodge machine simulation of the Belousov-Zhabotinsky reaction

One of the simplest multilevel cellular automata - the hodgepodge machine - was modified to best match the chemical trajectory observed in the Belousov-Zhabotinsky reaction. Noise introduces watersheding of the central regular pattern into the circular target pattern. This article analyzes influences of the neighborhood and internal excitation kinds of noise. We have found that configurations of ignition points, which give circular waves - target patterns, occur only in the interval of the neighborhood excitation noise from 30% to 34% and at the internal excitation noise of 12%. Noisy hodgepodge machine with these parameters is the best approximation to the experimental Belousov-Zhabotinsky reaction.

nlin.CG↗

arXiv2016

Model of the Belousov-Zhabotinsky reaction

The article describes results of the modified model of the Belousov-Zhabotinsky reaction, which resembles rather well the limit set observed upon experimental performance of the reaction in the Petri dish. We discuss the concept of the ignition of circular waves and show that only the asymmetrical ignition leads to the formation of spiral structures. From the qualitative assumptions on the behavior of dynamic systems, we conclude that the Belousov-Zhabotinsky reaction likely forms a regular grid.

nlin.CG↗

arXiv2015

Model of the Belousov-Zhabotinsky reaction Part 2: Central role of the internal excitationgrowth rate

The model of the Belousov-Zhabotinsky reaction, so-called hodgepodge machine, is discussed in detail and compared with the experimentally determined system trajectory. We show that many of the features observed in the experiment may be found at different internal excitation growth rates, the g/maxState ratios. The g/maxState ratio determines the structure of the limit set and defines also details of the system state-space trajectory. While the limit set identical to the experiment and the model may be found, there is not a single g/maxState level which defines the trajectory identical to the experiment. We also propose that there is an inherent experimental time unit defined by the time extent of the bottleneck chemical reaction process which defines the g/maxState ratio and the spatial element of the process.

nlin.CG↗

arXiv2010

Technical performance and interpretation of physical experiment in problems of cell biology

The lecture summarises main results of my team over last five years in the field of technical experiment design and interpretation of results of experiments for cell bi-ology. I introduce the theoretical concept of the experiment, based mainly on ideqas of stochastic systems theory, and confront it with general ideas of systems theory. In the next part I introduce available experiments and discuss their information con-tent. Namely, I show that light microscopy may be designed to give resolution com-parable to that of electron microscopy and that may be used for experiments using living cells. I show avenues to objective analysis of cell behavior observation. I pro-pose new microscope design, which shall combine advantages of all methods, and steps to be taken to build a model of living cells with predictive power for practical use

q-bio.OT↗

arXiv2010

Georg de Buquoy - Founder of Mathematical Economy with South Bohemian Roots

Georg de Buquoy, Lord de Vaux, lived in Nove Hrady, Prague and Cerveny Hradek for most of his productive life. From his extensive scientific contributions, both theoretical and experimental, we expand here the discussion of his contributions to mathematical economy. He is mainly celebrated as the first persons to define correctly net yield and describe method for its optimization, which was considered "strikingly modern" still in 1950. Buquoy's program was "systematic overview of all theorems which affect maintenance and increase of national wealth" for which he correctly defined and mathematically expressed many economic terms. The most striking feature of Buquoy's writing is that he was also a very influential economic practitioner. He governed one of the wealthiest possessions in Bohemia, and perhaps in Austria, of his time. Thus his economical thinking expands from the "political part", which is economy in modern sense, to "...sources of national wealth, or the technical part of national economy ...". The complexity of Buquoy's view has little match in modern literature namely because the extent of data sources is hardly available in modern times. The article puts Buquoy's mathematical economy contributions in context to his mathematical physics thoughts and approaches. The last direct citation of Buquoy's work comes from the year 2008.

physics.hist-ph↗