The use of 3D visualization technologies has increased rapidly in many applied fields, including geovisualization, and has been researched from many different perspectives. However, the findings for the benefits of 3D visualization, especially in stereoscopic 3D forms, remain inconclusive and disputed. Stereoscopic "real" 3D visualization was proposed as encouraging the visual perception of shapes and volume of displayed content yet criticised as problematic and limited in a number of ways, particularly in visual discomfort and increased response time in tasks. In order to assess the potential of real 3D visualization for geo-applications, 91 participants were engaged in this study to work with digital terrain models in different 3D settings. The researchers examined the effectivity of stereoscopic real 3D visualization compared to monoscopic 3D (or pseudo 3D) visualization under static and interactive conditions and applied three tasks with experimental stimuli representing different geo-related phenomena, i.e. objects in the terrain, flat areas marked in the terrain and terrain elevation profiles. The authors explored the significant effects of real 3D visualization and interactivity factors in terms of response time and correctness. Researchers observed that the option to interact (t = -10.849, p < 0.001) with a virtual terrain and its depiction with real 3D visualization (t = 4.64, p < 0.001) extended the participants' response times. Counterintuitively, the data demonstrated that the static condition increased response correctness (z = 5.38, p < 0.001). Regarding detailed analysis of data, an interactivity factor was proposed as a potential substitute for real 3D visualization in 3D geographical tasks.

• MeSH
• dospělí MeSH
• geografická kartografie * MeSH
• lidé středního věku MeSH
• lidé MeSH
• lineární modely MeSH
• mladý dospělý MeSH
• počítačová grafika MeSH
• reakční čas MeSH
• zeměpis metody   statistika a číselné údaje   MeSH
• zobrazování trojrozměrné metody   statistika a číselné údaje   MeSH
• zraková percepce MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Angiogenesis is the process of new blood vessels growing from existing vasculature. Visualizing them as a three-dimensional (3D) model is a challenging, yet relevant, task as it would be of great help to researchers, pathologists, and medical doctors. A branching analysis on the 3D model would further facilitate research and diagnostic purposes. In this paper, a pipeline of vision algorithms is elaborated to visualize and analyze blood vessels in 3D from formalin-fixed paraffin-embedded (FFPE) granulation tissue sections with two different staining methods. First, a U-net neural network is used to segment blood vessels from the tissues. Second, image registration is used to align the consecutive images. Coarse registration using an image-intensity optimization technique, followed by finetuning using a neural network based on Spatial Transformers, results in an excellent alignment of images. Lastly, the corresponding segmented masks depicting the blood vessels are aligned and interpolated using the results of the image registration, resulting in a visualized 3D model. Additionally, a skeletonization algorithm is used to analyze the branching characteristics of the 3D vascular model. In summary, computer vision and deep learning is used to reconstruct, visualize and analyze a 3D vascular model from a set of parallel tissue samples. Our technique opens innovative perspectives in the pathophysiological understanding of vascular morphogenesis under different pathophysiological conditions and its potential diagnostic role.

• Klíčová slova
• 3D visualization, angiogenesis, artificial intelligence, biobanking, digital pathology, image registration and segmentation, neural networks,
• MeSH
• algoritmy MeSH
• kardiovaskulární fyziologické jevy MeSH
• morfogeneze MeSH
• neuronové sítě * MeSH
• počítačové zpracování obrazu MeSH
• zobrazování trojrozměrné * metody   MeSH
• Publikační typ
• časopisecké články 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.

• Klíčová slova
• 3D object segmentation, 3D super-resolution microscopy, Delaunay algorithm, Mitochondrial DNA replication, Nucleoids, Principal component analysis,
• 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
• Názvy látek
• DNA vazebné proteiny MeSH
• mitochondriální DNA MeSH
• mitochondriální proteiny MeSH
• NABP2 protein, human MeSH Prohlížeč

The representation of carbohydrates in 3D space using symbols is a powerful visualization method, but such representations are lacking in currently available visualization software. The work presented here allows researchers to display carbohydrate 3D structures as 3D-SNFG symbols using LiteMol from a web browser (e.g., v.litemol.org/?loadFromCS=5T3X ). Any PDB ID can be substituted at the end of the URL. Alternatively, the user may enter a PDB ID or upload a structure. LiteMol is available at https://v.litemol.org and automatically depicts any carbohydrate residues as 3D-SNFG symbols. To embed LiteMol in a webpage, visit https://github.com/dsehnal/LiteMol .

• Klíčová slova
• 3D-SNFG, LiteMol, SNFG, carbohydrate, glycan, glycoprotein, oligosaccharide, structure, symbol nomenclature for glycans, visualization,
• MeSH
• molekulární konformace * MeSH
• polysacharidy chemie   MeSH
• sacharidy chemie   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• polysacharidy MeSH
• sacharidy MeSH

This paper describes a new tool for eye-tracking data and their analysis with the use of interactive 3D models. This tool helps to analyse interactive 3D models easier than by time-consuming, frame-by-frame investigation of captured screen recordings with superimposed scanpaths. The main function of this tool, called 3DgazeR, is to calculate 3D coordinates (X, Y, Z coordinates of the 3D scene) for individual points of view. These 3D coordinates can be calculated from the values of the position and orientation of a virtual camera and the 2D coordinates of the gaze upon the screen. The functionality of 3DgazeR is introduced in a case study example using Digital Elevation Models as stimuli. The purpose of the case study was to verify the functionality of the tool and discover the most suitable visualization methods for geographic 3D models. Five selected methods are presented in the results section of the paper. Most of the output was created in a Geographic Information System. 3DgazeR works with the SMI eye-tracker and the low-cost EyeTribe tracker connected with open source application OGAMA, and can compute 3D coordinates from raw data and fixations.

• Klíčová slova
• 3D analysis tool, 3D model, 3D visualization, Geographic Information System, cartography, eye-tracking,
• Publikační typ
• časopisecké články MeSH

Cell culture methods have been developed in efforts to produce biologically relevant systems for developmental and disease modeling, and appropriate analytical tools are essential. Knowledge of ultrastructural characteristics represents the basis to reveal in situ the cellular morphology, cell-cell interactions, organelle distribution, niches in which cells reside, and many more. The traditional method for 3D visualization of ultrastructural components, serial sectioning using transmission electron microscopy (TEM), is very labor-intensive due to contentious TEM slice preparation and subsequent image processing of the whole collection. In this chapter, we present serial block-face scanning electron microscopy, together with complex methodology for spheroid formation, contrasting of cellular compartments, image processing, and 3D visualization. The described technique is effective for detailed morphological analysis of stem cell spheroids, organoids, as well as organotypic cell cultures.

• Klíčová slova
• 3D visualization, Image reconstruction, Image segmentation, Morphology, Organoid, SBF-SEM, Scanning electron microscopy, Serial block-face, Spheroid, Stem cell, Ultrastructure,
• MeSH
• buněčné sféroidy ultrastruktura   MeSH
• embryonální kmenové buňky ultrastruktura   MeSH
• kultivované buňky MeSH
• lidé MeSH
• mikroskopie elektronová rastrovací metody   MeSH
• počítačové zpracování obrazu MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This paper focuses on the method for creating 3-dimensional (3D) digital models extracted from patient- specific scans of the brain. The described approach consists of several cross-platform stages: raw data segmentation, data correction in 3D-modelling software, post-processing of the 3D digital models and their presentation on an interactive web-based platform. This method of data presentation offers a cost and time effective option to present medical data accurately. An important aspect of the process is using real patient data and enriching the traditional slice-based representation of the scans with 3D models that can provide better understanding of the organs' structures. The resulting 3D digital models also form the basis for further processing into different modalities, for example models in Virtual Reality or 3D physical model printouts. The option to make medical data less abstract and more understandable can extend their use beyond diagnosis and into a potential aid in anatomy and patient education. The methods presented in this paper were originally based on the master thesis 'Transparent Minds: Testing for Efficiency of Transparency in 3D Physical and 3D Digital Models', which focussed on creating and comparing the efficiency of transparent 3D physical and 3D digital models from real-patient data.

• Klíčová slova
• 3D models, Alzheimer’s disease, data segmentation, medical art, medical visualization, patient data,
• MeSH
• anatomické modely * MeSH
• lidé MeSH
• mozek MeSH
• software MeSH
• virtuální realita * MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Our goal was to find an optimal tissue clearing protocol for whole-mount imaging of embryonic and adult hearts and whole embryos of transgenic mice that would preserve green fluorescent protein GFP fluorescence and permit comparison of different currently available 3D imaging modalities. We tested various published organic solvent- or water-based clearing protocols intended to preserve GFP fluorescence in central nervous system: tetrahydrofuran dehydration and dibenzylether protocol (DBE), SCALE, CLARITY, and CUBIC and evaluated their ability to render hearts and whole embryos transparent. DBE clearing protocol did not preserve GFP fluorescence; in addition, DBE caused considerable tissue-shrinking artifacts compared to the gold standard BABB protocol. The CLARITY method considerably improved tissue transparency at later stages, but also decreased GFP fluorescence intensity. The SCALE clearing resulted in sufficient tissue transparency up to ED12.5; at later stages the useful depth of imaging was limited by tissue light scattering. The best method for the cardiac specimens proved to be the CUBIC protocol, which preserved GFP fluorescence well, and cleared the specimens sufficiently even at the adult stages. In addition, CUBIC decolorized the blood and myocardium by removing tissue iron. Good 3D renderings of whole fetal hearts and embryos were obtained with optical projection tomography and selective plane illumination microscopy, although at resolutions lower than with a confocal microscope. Comparison of five tissue clearing protocols and three imaging methods for study of GFP mouse embryos and hearts shows that the optimal method depends on stage and level of detail required.

• Klíčová slova
• Confocal microscopy, Embryo, Green fluorescent protein (GFP), Heart, Optical projection tomography, Tissue transparency,
• MeSH
• myši transgenní MeSH
• myši MeSH
• srdce embryologie   MeSH
• zelené fluorescenční proteiny analýza   biosyntéza   genetika   MeSH
• zobrazování trojrozměrné metody   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Názvy látek
• zelené fluorescenční proteiny MeSH

Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/.

• MeSH
• internet * MeSH
• konformace proteinů MeSH
• proteiny * chemie   ultrastruktura   MeSH
• virtuální realita * MeSH
• výpočetní biologie metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• proteiny * MeSH

The aim of this study was to determine whether capillarity in the denervated and reinnervated rat extensor digitorum longus muscle (EDL) is scaled by muscle fiber oxidative potential. We visualized capillaries adjacent to a metabolically defined fiber type and estimated capillarity of fibers with very high oxidative potential (O) vs fibers with very low oxidative potential (G). Capillaries and muscle fiber types were shown by a combined triple immunofluorescent technique and the histochemical method for NADH-tetrazolium reductase. Stacks of images were captured by a confocal microscope. Applying the Ellipse program, fibers were outlined, and the diameter, perimeter, cross-sectional area, length, surface area, and volume within the stack were calculated for both fiber types. Using the Tracer plug-in module, capillaries were traced within the three-dimensional (3D) volume, the length of capillaries adjacent to individual muscle fibers was measured, and the capillary length per fiber length (Lcap/Lfib), surface area (Lcap/Sfib), and volume (Lcap/Vfib) were calculated. Furthermore, capillaries and fibers of both types were visualized in 3D. In all experimental groups, O and G fibers significantly differed in girth, Lcap/Sfib, and Lcap/Vfib, but not in Lcap/Lfib. We conclude that capillarity in the EDL is scaled by muscle fiber size and not by muscle fiber oxidative potential.

• MeSH
• denervace svalu MeSH
• histocytochemie MeSH
• kapiláry anatomie a histologie   MeSH
• konfokální mikroskopie MeSH
• kosterní svalová vlákna metabolismus   MeSH
• kosterní svaly krevní zásobení   inervace   metabolismus   MeSH
• krysa rodu Rattus MeSH
• oxidace-redukce MeSH
• potkani Wistar MeSH
• zobrazování trojrozměrné MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH