Současná zdravotnická technika produkuje každým okamžikem velké objemy dat. Výsledkem je informační přetížení a nemožnost zvládnout tato enormní data, např. na odd. intenzivní péče. Nástroje pro vizualizaci dat mají za cíl zmenšit toto informační přetížení pomocí inteligentní abstrakce a vizualizace zajímavých atributů zpracovávaných dat. Nově vyvíjené soft - warové nástroje pro vizualizaci by měly podporovat rychlé porozumění složitým, rozsáhlým a dynamicky rostoucím datovým souborům ve všech oblastech medicíny. Jednou z takových oblastí je analýza a vyhodnocování dlouhodobých záznamů EEG. S vyhodnocováním EEG je spojena celá řada problémů. Jedním z nich je potřeba vizuální kontroly záznamu lékařem. V případě, že lékař musí kontrolovat a hodnotit dlouhodobý záznam EEG, je počítačová podpora analýzy a vizualizace velkou pomocí. Právě možnosti vizualizace EEG záznamů a procesu jejich analýzy jsou předmětem našeho příspěvku.

Healthcare technology produces today large sets of data every second. An information overload results from these enormous data volumes not manageable by physicians, e.g. in intensive care. Data visualization tools aim at reducing the information overload by intelligent abstraction and visualization of the features of interest in the current situation. Newly developed soft - ware tools for visualization should support fast comprehension of complex, large, and dynamically growing datasets in all fi elds of medicine. One of such fi elds is the analysis and evaluation of long–term EEG recordings. One of the problems that are connected with the evaluation of EEG signals is that it necessitates visual checking of such a recording performed by a physician. In case the physician has to check and evaluate long–term EEG recordings computer–aided data analysis and visualization might be of great help. Soft ware tools for visualization of EEG data and data analysis are presented in the paper.

• MeSH
• algoritmy MeSH
• anatomické modely MeSH
• elektroencefalografie využití   MeSH
• epilepsie diagnóza   MeSH
• financování organizované MeSH
• klasifikace MeSH
• kóma diagnóza   patofyziologie   MeSH
• lidé MeSH
• mapování mozku metody   přístrojové vybavení   MeSH
• modely neurologické MeSH
• neuronové sítě MeSH
• počítačové zpracování signálu přístrojové vybavení   MeSH
• shluková analýza MeSH
• spánek fyziologie   MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• lidé MeSH

For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.

• MeSH
• počítačové zpracování obrazu * MeSH
• software * MeSH
• umělá inteligence * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

• MeSH
• počítačová grafika * MeSH
• počítačová simulace MeSH
• počítačové zpracování obrazu MeSH
• Publikační typ
• periodika MeSH

• Konspekt
• Počítačová věda. Výpočetní technika. Informační technologie
• NLK Obory
• technika

Protein structures contain highly complex systems of voids, making up specific features such as surface clefts or grooves, pockets, protrusions, cavities, pores or channels, and tunnels. Many of them are essential for the migration of solvents, ions and small molecules through proteins, and their binding to the functional sites. Analysis of these structural features is very important for understanding of structure-function relationships, for the design of potential inhibitors or proteins with improved functional properties. Here we critically review existing software tools specialized in rapid identification, visualization, analysis and design of protein tunnels and channels. The strengths and weaknesses of individual tools are reported together with examples of their applications for the analysis and engineering of various biological systems. This review can assist users with selecting a proper software tool for study of their biological problem as well as highlighting possible avenues for further development of existing tools. Development of novel descriptors representing not only geometry, but also electrostatics, hydrophobicity or dynamics, is needed for reliable identification of biologically relevant tunnels and channels.

• MeSH
• konformace proteinů MeSH
• molekulární modely * MeSH
• proteiny chemie   metabolismus   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.

• MeSH
• software * MeSH
• systémová biologie * MeSH
• Publikační typ
• časopisecké články MeSH

• MeSH
• analýza dat MeSH
• Publikační typ
• kongresy MeSH
• sborníky MeSH

• Konspekt
• Biologické vědy
• NLK Obory
• lékařská informatika

Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary information: Supplementary data are available at Bioinformatics online.

• MeSH
• algoritmy MeSH
• konformace proteinů MeSH
• proteinové inženýrství MeSH
• proteiny chemie   MeSH
• simulace molekulární dynamiky * MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

UNLABELLED: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. AVAILABILITY AND IMPLEMENTATION: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz.

• MeSH
• ligandy MeSH
• počítačová grafika * MeSH
• proteiny chemie   metabolismus   MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• vazebná místa MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.

• MeSH
• algoritmy * MeSH
• analýza hlavních komponent * MeSH
• buňky Hep G2 MeSH
• DNA vazebné proteiny metabolismus   MeSH
• fluorescenční mikroskopie * MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• mitochondriální DNA chemie   metabolismus   MeSH
• mitochondriální proteiny metabolismus   MeSH
• molekulární modely MeSH
• zobrazování trojrozměrné * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Hypoparatyreóza s hypokalcemií je jednou z nejčastějších komplikací operací štítné žlázy. Od roku 2022 využíváme ve Vojenské nemocnici v Brně peroperační vizualizaci příštítných tělísek (PT) pomocí autofluorescenčního systému Fluoptics, Fluobeam® LX (FF®). Cílem práce je prezentovat princip této metody a zhodnotit přínos pro operatéry a pacienty. Materiál a metody: Během každé operace štítné žlázy používáme systém FF®, který na podkladě fluorescenčních vlastností příštítných tělísek umožňuje jejich časnou peroperační detekci. Retrospektivní analýzou posuzujeme přínos této metody pro naše pracoviště. Sledujeme vliv zapojení systému FF® během tyreoidálních výkonů na snížení incidence neúmyslného odstranění PT, pokles výskytu pooperační hypokalcemie a vliv použití FF® na délku operace. Výsledky: Bylo hodnoceno celkem 309 pacientů. Soubor operovaných bez využití FF® zahrnoval 163 pacientů, soubor s použitím FF® 146 pacientů. PT bylo v souboru bez FF® neúmyslně odstraněno v 16,6 %, v souboru s FF® v 4,1 % případů. Pokles hladiny sérového vápníku < 2,00 mmol/l v pooperačním období jsme zaznamenali v souboru bez FF® v 18,4 %, v souboru s FF® ve 13,7 %. Pokles hladiny vápníku s nutnou dlouhodobou substitucí byl v souboru bez FF® 5,5 %, v souboru s FF® 0,7 %. Průměrná doba trvání totální tyreoidektomie s použitím FF® se prodloužila o 10,9 min, doba trvání hemityreoidektomie se prodloužila o 2,4 min. Závěr: Dosavadní zkušenosti s peroperačním fluorescenčním zobrazením příštítných tělísek na našem pracovišti prokazují významný pokles incidence nechtěného odstranění PT. Snížení výskytu dočasné i trvalé hypokalcemie nebylo statisticky významné. Celková doba operace se prodloužila v řádu jednotek minut.

Hypoparathyroidism with hypocalcemia is one of the most common complications of thyroid surgery. Since 2022, at the Military Hospital Brno, we have been using intraoperative visualization of the parathyroid glands (PG) with Fluoptics, Fluobeam® LX (FF®) autofluorescence system. We would like to present the principle of this method and evaluate the benefits for surgeons and patients. Materials and methods: During thyroid surgery, we use the FF® system, which based on the fluorescent properties of PG, enables early intraoperative detection. Through a retrospective analysis, we assess the benefit of this method-especially the effect of using the FF® system during thyroid procedures on the reduction of the incidence of inadvertent resection of PG, the decrease in the incidence of postoperative hypocalcemia, and the effect of the use of FF® for the duration of the operation. Results: A total of 309 patients were evaluated. The group of patients operated without using FF® included 163 patients, and the group using FF® included 146 patients. PG was unintentionally removed in 16.6% of cases in the group without using FF®, and in 4.1% of cases in the group using FF®. A drop in the serum calcium level below 2.00 mmol/ l was registered during the postoperative period in 18.4% in the group without using FF® and 13.7% in the group using FF®. Long-term calcium substitution was necessary in 5.5% cases in the group without using FF®, and 0.7% in the group using FF®. The average duration of total thyroidectomy using FF® increased by 10.9 minutes, and the duration of hemithyroidectomy increased by 2.4 minutes. Conclusion: According to our experience, intraoperative fluorescence imaging confi rms a decrease in the incidence of inadvertent resection of PG. Reduction in the incidence of temporary and permanent hypocalcemia was not significant. The mean operative time was extended in units of minutes.

• MeSH
• dospělí MeSH
• fluorescence MeSH
• hypokalcemie krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• optické zobrazování * metody   MeSH
• paratyreoidea * diagnostické zobrazování   MeSH
• retrospektivní studie MeSH
• senioři MeSH
• tyreoidektomie metody   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH