25 papers · ranked by Valyu relevance
Fuhui Long, Jianlong Zhou, Hanchuan Peng, Fran Lewitter
In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key…
Sara Rolfe, Steve Pieper, Arthur Porto, Kelly Diamond + 6 more
Large scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. MorphoSource currently hosts…
Rafał Kaźmierczak, Agnieszka Szczepańska
Spatial planning and development use various visualisation methods. Technological advancements in visualisation techniques have allowed imaging to shift from 2 to 3D dimensions. 3D optical illusion, which converts information recorded in the digital form into a three-dimensional presentation, can be a new tool for…
David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already…
Philip M. Hubbard, Stuart Berg, Ting Zhao, Donald J. Olbris + 6 more
Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While…
Roberta Cabral Mota, Allan Rocha, Julio Daniel Silva, Usman Alim + 1 more
In 3D visualizations, data is often represented as a combination of geometric representations (e.g., points, streamlines, surfaces), with associated attributes. To present data across multiple representations brings on the need for investigating the (inter-relations of) different data types to obtain an integrated…
Wei Zhang, Jonathan A Fine, Christopher Sculley, Jordon McGraw + 1 more
The representation of complex biomolecular structures and interactions is a difficult challenge across life sciences. Researchers and students use unintuitive 2D representations to gain an intuitive understanding of 3D space and molecular interactions. Since this is cumbersome for complex structures, such as…
Kevin A. Yamauchi, Alister Burt
With recent advances in three-dimensional bioimaging acquisition and analysis methods, imaging data are an important tool for unveiling the complex architecture of biological organisms. However, extracting insights from these complex datasets requires interactive exploration as well as annotation for training…
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa + 9 more
Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established^1,2^ and its wide-spread adoption has led to the development of more than 36 software packages, dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching^3^.…
David G. Barnes, Michail Vidiassov, Bernhard Ruthensteiner, Christopher J. Fluke + 3 more
'Christopher J. Fluke' 'Michelle R. Quayle' 'Colin R. McHenry' 'Kewei Chen'] With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper…
Shuo Han, Alain Chen, Soonam Lee, Chichen Fu + 7 more
The advancement of high content optical microscopy has enabled the acquisition of very large 3D image datasets. Image analysis tools and three dimensional visualization are critical for analyzing and interpreting 3D image volumes. The analysis of these volumes require more computational resources than a biologist may…
Anas M. Al-Oraiqat, Sergey A. Zori
- This paper presents a realization of the approach to spatial 3D stereo of visualization of 3D images with use parallel Graphics processing unit (GPU). The experiments of realization of synthesis of images of a 3D stage by a method of trace of beams on GPU with Compute Unified Device Architecture (CUDA) have shown…
Claudine Métral, Nizar Ghoula, Gilles Falquet
3D city models - which represent in 3 dimensions the geometric elements of a city - are increasingly used for an intended wide range of applications. Such uses are made possible by using semantically enriched 3D city models and by presenting such enriched 3D city models in a way that allows decision-making processes to…
Paula C. Sanematsu
The development of physics-based 3D models that investigate the behavior of biological tissues requires effective and efficient visualization tools. The open-source software ParaView has such capabilities, but often impose a steep learning curve due to the use of the Visualization Toolkit (VTK) data structures. To…
Hootan Roshandel, Matthew Shammami, Shiyun Lin, Yin-Pok Wong + 1 more
The rise of virtual and online education in recent years has led to the development and popularization of many online tools, notably 3D models and augmented reality (AR), for visualizing various structures in chemical sciences. The majority of the developed tools focus on either small molecules or biological systems…
Authors not listed
For decades, molecular visualization software has been fundamental to education and research in chemistry, structural biology, and materials science. These tools have enabled the inspection of structures, dynamics, and interactions, yet their reliance on two-dimensional (2D) interfaces imposes persistent limitations.…
Linglong Zhou, Guoxin Wu, Yunbo Zuo, Xuanyu Chen + 2 more
With the rapid development of 3D reconstruction, especially the emergence of algorithms such as NeRF and 3DGS, 3D reconstruction has become a popular research topic in recent years. 3D reconstruction technology provides crucial support for training extensive computer vision models and advancing the development of…
Anas M. Al-Oraiqat, Yevgen Bashkov, Sergey A. Zori, Aladdein M. Amro
A general concept of 3D volumetric visualization systems is described based on 3D discrete voxel scenes (worlds) representation. Definitions of 3D discrete voxel scene (world) basic elements and main steps of the image synthesis algorithm are formulated. An algorithm for solving the problem of the voxelized world 3D…
Enrique Canessa, Livio Tenze
We developed a method to transform stereoscopic two-dimensional (2D) images into holograms via unsupervised morphing deformations between left (L) and right (R) input images. By using robust DeepFlow and light-field rendering algorithms, we established correlations between a 2D scene and its three-dimensional (3D)…
Claudine Métral, Gilles Falquet
When creating 3D city models, selecting relevant visualization techniques is a particularly difficult user interface design task. A first obstacle is that current geodata-oriented tools, e.g. ArcGIS, have limited 3D capabilities and limited sets of visualization techniques. Another important obstacle is the lack of…
Haruki Fukuda, Lars Ebert, Florian Kreitmeier, Sebastian Eggert + 4 more
The accurate documentation of bodies, injuries, death scenes, accidents, and crime scenes is fundamental to forensic investigations. Traditional two-dimensional (2D) photography and written reports have inherent limitations in representing complex spatial relationships. Recently, three-dimensional (3D) surface…
Wenhui Zhang
Medical visualization is the use of computers to create 3D images from medical imaging data sets, almost all surgery and cancer treatment in the developed world relies on it.Volume visualization techniques includes iso-surface visualization, mesh visualization and point cloud visualization techniques, these techniques…
Anas M. Al-Oraiqat, Sergey A. Zori
This article discusses the study of 3D graphic volume primitive computer system generation (3D segments) based on General Purpose Graphics Processing Unit (GPGPU) technology for 3D volume visualization systems. It is based on the general method of Volume 3D primitive generation and an algorithm for the voxelization of…
Murat Cihan Sorkun, Dajt Mullaj, J. M. Vianney A. Koelman, Süleyman Er
Visualizing chemical spaces streamlines the analysis of molecular datasets by reducing the information to human perception level, hence it forms an integral piece of molecular engineering, including chemical library design, high-throughput screening, diversity analysis, and outlier detection. We present here ChemPlot…
Kelsey Hatzell, Yanjie Zheng
X-ray Computed Tomography (CT) is a non-invasive, non-destructive approach to imaging materials, material systems and engineered components in two- and three- dimensions. Acquisition of 3D images requires the collection of hundreds or thousands of through-thickness X-ray radiographic images from different angles. Such…