This study aimed to compare the fascicular anatomy of upper limb nerves visualized using in situ high-resolution ultrasound (HRUS) with ex vivo imaging modalities, namely, magnetic resonance microscopy (MRM), histological cross-sections (HCS), and optical projection tomography (OPT). The median, ulnar, and superficial branch of radial nerve (n = 41) were visualized in 14 cadaveric upper limbs using 22-MHz HRUS. Subsequently, the nerves were excised, imaged with different microscopic techniques, and their morphometric properties were compared. HRUS accurately differentiated 51-74% of fascicles, while MRM detected 87-92% of fascicles when compared to the referential HCS. Among the compared modalities, HRUS demonstrated the smallest fascicular ratios and fascicular cross-sectional areas, but the largest nerve cross-sectional areas. The probability of a fascicle depicted on HRUS representing a cluster of multiple fascicles on the referential HCS increased with the fascicular size, with some differences observed between the larger median and ulnar nerves and the smaller radial nerves. Accordingly, HRUS fascicle differentiation necessitates cautious interpretation, as larger fascicles are more likely to represent clusters. Although HCS is considered the reference modality, alterations in nerve cross-sectional areas or roundness during sample processing should be acknowledged.

• Klíčová slova
• Fascicle differentiation, MR neurography, Nerve anatomy, Peripheral nerve imaging, Ultrasonography,
• MeSH
• horní končetina * inervace   diagnostické zobrazování   MeSH
• lidé středního věku MeSH
• lidé MeSH
• magnetická rezonanční tomografie metody   MeSH
• mikroskopie metody   MeSH
• mrtvola MeSH
• nervus medianus diagnostické zobrazování   MeSH
• nervus radialis * diagnostické zobrazování   anatomie a histologie   MeSH
• nervus ulnaris * diagnostické zobrazování   anatomie a histologie   MeSH
• senioři MeSH
• ultrasonografie * metody   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

An important issue in the context of both potenial toxicity of iron oxide nanoparticles (IONP) and their medical applications is tracking of the internalization process of these nanomaterials into living cells, as well as their localization and fate within them. The typical methods used for this purpose are transmission electron microscopy, confocal fluorescence microscopy as well as light-scattering techniques including dark-field microscopy and flow cytometry. All the techniques mentioned have their advantages and disadvantages. Among the problems it is necessary to mention complicated sample preparation, difficult interpretation of experimental data requiring qualified and experienced personnel, different behavior of fluorescently labeled IONP comparing to those label-free or finally the lack of possibility of chemical composition characteristics of nanomaterials. The purpose of the present investigation was the assessment of the usefulness of Raman microscopy for the tracking of the internalization of IONP into cells, as well as the optimization of this process. Moreover, the study focused on identification of the potential differences in the cellular fate of superparamagnetic nanoparticles having magnetite and maghemite core. The Raman spectra of U87MG cells which internalized IONP presented additional bands which position depended on the used laser wavelength. They occurred at the wavenumber range 1700-2400 cm-1 for laser 488 nm and below the wavenumber of 800 cm-1 in case of laser 532 nm. The intensity of the mentioned Raman bands was higher for the green laser (532 nm) and their position, was independent and not characteristic on the primary core material of IONP (magnetite, maghemite). The obtained results showed that Raman microscopy is an excellent, non-destructive and objective technique that allows monitoring the process of internalization of IONP into cells and visualizing such nanoparticles and/or their metabolism products within them at low exposure levels. What is more, the process of tracking IONP using the technique may be further improved by using appropriate wavelength and power of the laser source.

• Klíčová slova
• Internalization into cells, Iron oxide nanoparticles, Magnetite and maghemite core, Multivariate methods, Raman spectroscopy and imaging,
• MeSH
• lidé MeSH
• magnetické nanočástice oxidů železa * chemie   MeSH
• mikroskopie metody   MeSH
• nádorové buněčné linie MeSH
• Ramanova spektroskopie * metody   MeSH
• železité sloučeniny chemie   analýza   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• železité sloučeniny MeSH

We present two cases from the neonatal department with cerebrospinal fluid examination. We revealed a striking discrepancy in polymorphonuclear (PMN) and mononuclear (MN) cell counts using conventional light microscopy in comparison with automated analyzer Sysmex XN-1000 (PMNs - 13 vs. 173x106/L, MNs - 200 vs. 67x106/L in case 1 and PMNs - 13 vs. 372x106/L, MNs - 411 vs. 179x106/L in case 2). We revealed the dominant presence of hemosiderophages in both cases in cytospin slide. Even though Sysmex XN-1000 offers fast examination with a low sample volume, there is possibility of misdiagnosis, with negative impact on the patient.

• Klíčová slova
• biochemistry, cerebrospinal fluid, cytology, hematology, neonatology,
• MeSH
• leukocyty mononukleární patologie   cytologie   MeSH
• lidé MeSH
• mikroskopie * metody   MeSH
• mozkomíšní mok cytologie   MeSH
• neutrofily cytologie   patologie   MeSH
• novorozenec MeSH
• počet leukocytů MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• srovnávací studie MeSH

Quantitative phase imaging (QPI) is a powerful tool for label-free visualisation of living cells. Here, we compare two QPI microscopes - the Telight Q-Phase microscope and the Nanolive 3D Cell Explorer-fluo microscope. Both systems provide unbiased information about cell morphology, such as individual cell dry mass, perimeter and area. The Q-Phase microscope uses artefact-free, coherence-controlled holographic imaging technology to visualise cells in real time with minimal phototoxicity. The 3D Cell Explorer-fluo employs laser-based holotomography to reconstruct 3D images of living cells, visualising their internal structures and dynamics. Here, we analysed the strengths and limitations of both microscopes when examining two morphologically distinct cell lines - the cuboidal epithelial MDCK cells which form multicellular clusters and solitary growing Rat2 fibroblasts. We focus mainly on the ability of the devices to generate images suitable for single-cell segmentation by the built-in software, and we discuss the segmentation results and quantitative data generated from the segmented images. We show that both microscopes offer slightly different advantages, and the choice between them depends on the specific requirements and goals of the user.

• Klíčová slova
• MDCK, Rat2, coherence-controlled holographic imaging/microscopy, dry mass content, holotomography, quantitative phase imaging/microscopy, single-cell segmentation,
• MeSH
• buněčné linie MeSH
• holografie * metody   MeSH
• kvantitativní fázové zobrazování MeSH
• lasery MeSH
• mikroskopie * metody   MeSH
• Publikační typ
• časopisecké články MeSH

Quantitative Phase Imaging is becoming an important tool in the objective evaluation of cellular responses to experimental treatment. The technique is based on interferometric measurements of the optical thickness of cells in tissue culture reporting on the distribution of dry mass inside the cells. As the measurement of the optical thickness is interferometric, it is not subjected to the Abbe resolution limit, and the use of an incoherent-light source further increases the accuracy practically achieving 0.93nm in optical path difference corresponding to 4.6 femtograms/μm2. Holographic mode reduces the exposure in comparison to phase-shifting or phase-stepping interference microscopy and allows observation of faster dynamics. An attractive application is in the development of novel anti-cancer drugs and there is an important potential for pretesting chemotherapeutic drugs with biopsy material for personalized cancer treatment. The procedure involves the preparation of live cells in tissue culture, seeding them into suitable observation chambers, and time-lapse recording with an adjusted microscope. Subsequent image processing and statistical analysis are essential last steps producing the results, which include rapid measurements of cell growth in terms of dry-mass increase in individual cells, speed of cell motility and other dynamic morphometric parameters.

• Klíčová slova
• Cancer cells, Holographic quantitative phase imaging, Light microscopy, Measurements of cell growth and motility,
• MeSH
• holografie * metody   MeSH
• mikroskopie metody   MeSH
• počítačové zpracování obrazu metody   MeSH
• pohyb buněk MeSH
• protinádorové látky * farmakologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• protinádorové látky * MeSH

Live cells act as biological lenses and can be employed as real-world optical components in bio-hybrid systems. Imaging at nanoscale, optical tweezers, lithography and also photonic waveguiding are some of the already proven functionalities, boosted by the advantage that cells are fully biocompatible for intra-body applications. So far, various cell types have been studied for this purpose, such as red blood cells, bacterial cells, stem cells and yeast cells. White Blood Cells (WBCs) play a very important role in the regulation of the human body activities and are usually monitored for assessing its health. WBCs can be considered bio-lenses but, to the best of our knowledge, characterization of their optical properties have not been investigated yet. Here, we report for the first time an accurate study of two model classes of WBCs (i.e., monocytes and lymphocytes) by means of a digital holographic microscope coupled with a microfluidic system, assuming WBCs bio-lens characteristics. Thus, quantitative phase maps for many WBCs have been retrieved in flow-cytometry (FC) by achieving a significant statistical analysis to prove the enhancement in differentiation among sphere-like bio-lenses according to their sizes (i.e., diameter d) exploiting intensity parameters of the modulated light in proximity of the cell optical axis. We show that the measure of the low intensity area (S: I z < I th z ) in a fixed plane, is a feasible parameter for cell clustering, while achieving robustness against experimental misalignments and allowing to adjust the measurement sensitivity in post-processing. 2D scatterplots of the identified parameters (d-S) show better differentiation respect to the 1D case. The results show that the optical focusing properties of WBCs allow the clustering of the two populations by means of a mere morphological analysis, thus leading to the new concept of cell-optical-fingerprint avoiding fluorescent dyes. This perspective can open new routes in biomedical sciences, such as the chance to find optical-biomarkers at single cell level for label-free diagnosis.

• Klíčová slova
• biolens, digital holographic cytometry, microfluidics, opto-biology, white blood cells,
• MeSH
• holografie * metody   MeSH
• lidé MeSH
• lymfocyty MeSH
• mikroskopie * metody   MeSH
• monocyty MeSH
• optika a fotonika MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Automatic detection and segmentation of biological objects in 2D and 3D image data is central for countless biomedical research questions to be answered. While many existing computational methods are used to reduce manual labeling time, there is still a huge demand for further quality improvements of automated solutions. In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility to biomedical data is largely unexplored. Here we introduce EmbedSeg, an embedding-based instance segmentation method designed to segment instances of desired objects visible in 2D or 3D biomedical image data. We apply our method to four 2D and seven 3D benchmark datasets, showing that we either match or outperform existing state-of-the-art methods. While the 2D datasets and three of the 3D datasets are well known, we have created the required training data for four new 3D datasets, which we make publicly available online. Next to performance, also usability is important for a method to be useful. Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. We believe that this renders EmbedSeg accessible to virtually everyone who requires high-quality instance segmentations in 2D or 3D biomedical image data.

• Klíčová slova
• Embeddings, Instance Segmentation, Microscopy,
• MeSH
• algoritmy * MeSH
• lidé MeSH
• mikroskopie * metody   MeSH
• počítačové zpracování obrazu metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Primary cilia are hair-like sensory organelles protruding from the surface of most human cells. As cilia are dynamic, several aspects of their biology can only be revealed by real-time analysis in living cells. Here we describe the generation of primary cilia reporter cell lines. Furthermore, we provide a detailed protocol of how to use the reporter cell lines for live-cell imaging microscopy analysis of primary cilia to study their growth as well as intraciliary transport. For complete details on the use and execution of this protocol, please refer to Bernatik et al. (2020) and Pejskova et al. (2020).

• Klíčová slova
• Cell Biology, Cell culture, Microscopy, Molecular Biology,
• MeSH
• buněčné linie MeSH
• cilie * metabolismus   MeSH
• lidé MeSH
• mikroskopie metody   MeSH
• počítačové zpracování obrazu * metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The incidence of death caused by cancer has been increasing worldwide. The growth of cancer cells is not the main problem. The majority of deaths are due to invasion and metastasis, where cancer cells actively spread from primary tumors. Our inbred rat model of spontaneous metastasis revealed dynamic phenotype changes in vitro correlating with the metastatic potential in vivo and led to a discovery of a metastasis suppressor, protein 4.1B, which affects their 2D motility on flat substrates. Subsequently, others confirmed 4.1B as metastasis suppressor using knock-out mice and patient data suggesting mechanism involving apoptosis. There is evidence that 2D motility may be differentially controlled to the 3D situation. Here we show that 4.1B affects cell motility in an invasion assay similarly to the 2D system, further supporting our original hypothesis that the role of 4.1B as metastasis suppressor is primarily mediated by its effect on motility. This is encouraging for the validity of the 2D analysis, and we propose Quantitative Phase Imaging with incoherent light source for rapid and accurate testing of cancer cell motility and growth to be of interest for personalized cancer treatment as illustrated in experiments measuring responses of human adenocarcinoma cells to selected chemotherapeutic drugs.

• MeSH
• invazivní růst nádoru * MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• mikroskopie metody   MeSH
• nádorové buněčné linie MeSH
• pohyb buněk * MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

A novel method for semiautomated assessment of directions of collagen fibers in soft tissues using histological image analysis is presented. It is based on multiple rotated images obtained via polarized light microscopy without any additional components, i.e., with just two polarizers being either perpendicular or nonperpendicular (rotated). This arrangement breaks the limitation of 90° periodicity of polarized light intensity and evaluates the in-plane fiber orientation over the whole 180° range accurately and quickly. After having verified the method, we used histological specimens of porcine Achilles tendon and aorta to validate the proposed algorithm and to lower the number of rotated images needed for evaluation. Our algorithm is capable to analyze 5·105 pixels in one micrograph in a few seconds and is thus a powerful and cheap tool promising a broad application in detection of collagen fiber distribution in soft tissues.

• MeSH
• Achillova šlacha metabolismus   MeSH
• algoritmy MeSH
• extracelulární matrix metabolismus   MeSH
• kolagen metabolismus   MeSH
• mikroskopie metody   MeSH
• optické zobrazování metody   MeSH
• počítačové zpracování obrazu metody   MeSH
• polarizační mikroskopie metody   MeSH
• prasata MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kolagen MeSH