Miroslav Jiřík

• University of West Bohemia

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In the field of histology, only a fraction of specimens are typically selected for quantification, requiring multilevel sampling or tissue probes, slides, and fields of view (FOVs) in regions of interest (ROIs). To ensure an unbiased sampling process across all levels, all parts of the organs under study should be given equal probability of inclusi...

Only a fraction of specimens under study are usually selected for quantification in histology. Multilevel sampling or tissue probes, slides and fields of view (FOVs) in the regions of interest (ROIs) are required. In general, all parts of the organs under study should be given the same probability to be taken into account; that is, the sampling sho...

Liver volumetry is an important tool in clinical practice. The calculation of liver volume is primarily based on Computed Tomography. Unfortunately, automatic segmentation algorithms based on handcrafted features tend to leak segmented objects into surrounding tissues like the heart or the spleen. Currently, convolutional neural networks are widely...

Decellularized tissue is an important source for biological tissue engineering. Evaluation of the quality of decellularized tissue is performed using scanned images of hematoxylin-eosin stained (H&E) tissue sections and is usually dependent on the observer. The first step in creating a tool for the assessment of the quality of the liver scaffold wi...

Annotating a dataset for training a Supervised Machine Learning algorithm is time and annotator’s attention intensive. Our goal was to create a tool that would enable us to create annotations of the dataset with minimal demands on expert’s time. Inspired by applications such as Tinder, we have created an annotation tool for describing microscopic i...

Decellularized scaffolds can serve as an excellent three-dimensional environment for cell repopulation. They maintain tissue-specific microarchitecture of extracellular matrix proteins with important spatial cues for cell adhesion, migration, growth, and differentiation. However, criteria for quality assessment of the three-dimensional structure of...

Currently, there are at least 70 pure domestic pig breeds, but only certain breeds are used in biomedical research. The domestic pig liver is suitable for preclinical research because its size, physiology, and anatomy are similar to that of the human liver; in addition, there is a high degree of genetic similarity between the two species. For plann...

The article is a step forward towards improving image segmentation using a popular method called Graph-Cut. We focus on optimizing the algorithm for processing data, in which the target object occupies only a small portion of the total volume. We propose a two-step procedure. At the first step, the location of the object is determined roughly. At t...

The pig is a large animal model that is often used in experimental medicine. The aim of this study was to assess, in normal pig livers, sexual dimorphism in the normal fraction of hepatic interlobular and intralobular connective tissue (CT) in six hepatic lobes and in three macroscopical regions of interest (ROIs) with different positions relative...

Aims: Micro-CT is a powerful and well-established method for non-destructive visualization and analysis in 2D and 3D. However, the verification of results obtained by micro-CT analysis of structural characteristics at micro-scale level is complicated and hard to achieve. Bias introduced by image noise, image processing (e.g. noise-reducing operatio...

Introduction: Sinusoidal obstruction syndrome (SOS) is a disease which is caused by toxic injury to hepatic sinusoids. This syndrome is most frequently caused by myeloablative radiochemotherapy in patients before hematopoietic stem cells transplantation and also by oxaliplatin mainly in patients with colorectal liver metastases. The aim of this st...

Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and poro...

A software to increase the reproducibility and reliability of research results when using micro-CT scans has been developed.

The paper summarizes our activities in modelling tissue perfusion using a multilevel approach which is based on information retrievable form CT and micro CT images. We focus on the liver tissue for which the perfusion modelling is of great interest for both medical research and clinical practice. The blood flow in liver is characterized at several...

Segmentation of internal organs from Computed Tomography images often uses intensity and shape properties. We introduce a navigation system based on robust segmentation of body tissues like spine, body surface and lungs. Pose estimation of an investigated tissue can be performed using this algorithm and it also can be used as a support information...

This paper provides summary of our experiments with automatic segmentation of liver parenchyma. It presents methods and classifiers that we used on computer tomography medicine data. In introduction there are a description of our motivation to do this research. Second part contains information about our approach, list of methods and classifiers. In...

This paper points out the main design goals of a novel representation scheme of geometric-topological data, named Linear Algebraic Representation (LAR), characterized by a wide domain, encompassing 2D and 3D meshes, manifold and non-manifold geometric and solid models, and high-resolution 3D images. To demonstrate its simplicity and effectiveness f...

Purpose: Quantitative description of hepatic microvascular bed could contribute to understanding perfusion CT imaging. Micro-CT is a useful method for the visualization and quantification of capillary-passable vascular corrosion casts. Our aim was to develop and validate open-source software for the statistical description of the vascular networks...

Quantitative analysis of histology slides can bring unique knowledge about the investigated sample. Unfortunately this is time consuming procedure. In this paper we suggest method to overcome this disadvantage. However, everything has its price. Semi-automatic evaluation cannot beat human operator by its precision, but it is able to process big amo...

We use a collection of Python programs for numerical simulation of liver perfusion. We have an application for semi-automatic generation of a finite element mesh of the human liver from computed tomography scans and for reconstruction of the liver vascular structure. When the real vascular trees can not be obtained from the CT data we generate arti...

Organ segmentation is often a first step in medical diagnostic. In this paper a fully automatic three-dimensional method for liver segmentation is presented. It is based on voxel density analysis with use of automated grow cut method. Obtained segmentation is then refined by active contours model.

This paper describes a method for texture based segmentation. Texture features are extracted by applying a bank of Gabor filters using two-sided convolution strategy. Probability texture model is represented by Gaussian mixture that is trained with the Expectation-maximization algorithm. Texture similarity, obtained this way, is used like the input...

This paper describes a solution of CT arteriography vessel segmentation using a combination of methods for segmentation of image data. Computer tomography (CT) is one of the most useful approaches for investigating the arterial system and its pathologies. There are three ways for segmenting the vessels from the CT image — manually, fully automatica...

This paper describes a method for texture based segmentation. Texture features are extracted by applying a bank of Gabor filters using two-sided convolution strategy. Probability texture model is represented by Gaussian mixture that is trained with the Expectation-maximization algorithm. Texture similarity, obtained this way, is used like the input...