We propose a new microscopy simulation system that can depict atomistic models in a micrograph visual style, similar to physical electron microscopy imaging results. This system is scalable, able to represent the simulation of electron microscopy of twenty complex viral particles, and synthesizes the image faster than previous approaches. Additionally, the simulator is differentiable in the deterministic and stochastic stages that form signal and noise representations in the micrograph. This allows for solving inverse problems by means of optimization and thus allows for the generation of microscopy simulations using parameter settings estimated from real data. We demonstrate this capability through two applications: (1) estimating the parameters of the modulation transfer function defining the detector properties of the simulated and real micrographs and (2) denoising the real data based on parameters optimized from the simulated examples using gradient descent. While current simulators do not support any parameter estimation due to their forward-only design, we show that the results obtained using estimated parameters are very similar to real micrographs. Additionally, we evaluate the denoising capabilities of our approach and show that the results are competitive with state-of-the-art methods. Denoised micrographs exhibit less noise in the tomographic reconstruction of tilt-series, facilitating visualization of microscopy tomography using direct volume rendering by reducing the visual dominance of noise.

Depth perception in volumetric visualization plays a crucial role in the understanding and interpretation of volumetric data. Numerous visualization techniques, many of which rely on physically based optical effects, promise to improve depth perception but often do so without considering camera movement or the content of the volume. As a result, the findings from previous studies may not be directly applicable to crowded volumes, where a large number of contained structures disrupts spatial perception. Crowded volumes therefore require special analysis and visualization tools with sparsification capabilities. Interactivity is an integral part of visualizing and exploring crowded volumes, but has received little attention in previous studies. To address this gap, we conducted a study to assess the impact of different rendering techniques on depth perception in crowded volumes, with a particular focus on the effects of camera movement. The results show that depth perception considering camera motion depends much more on the content of the volume than on the chosen visualization technique. Furthermore, we found that conventional non-photorealistic rendering techniques, which have often performed poorly in previous studies, showed comparable performance to modern photorealistic techniques in our study. The source code for the visualization system, survey, and analysis, as well as the data set used in the study and the participants’ responses, have been made publicly available.

Dr. KID is an algorithm that uses isometric decomposition for the physicalization of potato-shaped organic models in a puzzle fashion. The algorithm begins with creating a simple, regular triangular surface mesh of organic shapes, followed by iterative K-means clustering and remeshing. For clustering, we need similarity between triangles (segments) which is defined as a distance function. The distance function maps each triangle's shape to a single point in the virtual 3D space. Thus, the distance between the triangles indicates their degree of dissimilarity. K-means clustering uses this distance and sorts segments into k classes. After this, remeshing is applied to minimize the distance between triangles within the same cluster by making their shapes identical. Clustering and remeshing are repeated until the distance between triangles in the same cluster reaches an acceptable threshold. We adopt a curvature-aware strategy to determine the surface thickness and finalize puzzle pieces for 3D printing. Identical hinges and holes are created for assembling the puzzle components. For smoother outcomes, we use triangle subdivision along with curvature-aware clustering, generating curved triangular patches for 3D printing. Our algorithm was evaluated using various models, and the 3D-printed results were analyzed. Findings indicate that our algorithm performs reliably on target organic shapes with minimal loss of input geometry.

We present a novel framework for 3D tomographic reconstruction and visualization of tomograms from noisy electron microscopy tilt-series. Our technique takes as an input aligned tilt-series from cryogenic electron microscopy and creates denoised 3D tomograms using a proximal jointly-optimized approach that iteratively performs reconstruction and denoising, relieving the users of the need to select appropriate denoising algorithms in the pre-reconstruction or post-reconstruction steps. The whole process is accelerated by exploiting parallelism on modern GPUs, and the results can be visualized immediately after the reconstruction using volume rendering tools incorporated in the framework. We show that our technique can be used with multiple combinations of reconstruction algorithms and regularizers, thanks to the flexibility provided by proximal algorithms. Additionally, the reconstruction framework is open-source and can be easily extended with additional reconstruction and denoising methods. Furthermore, our approach enables visualization of reconstruction error throughout the iterative process within the reconstructed tomogram and on projection planes of the input tilt-series. We evaluate our approach in comparison with state-of-the-art approaches and additionally show how our error visualization can be used for reconstruction evaluation.

Abstract We present a novel smart visibility system for visualizing crowded volumetric data containing many object instances. The presented approach allows users to form groups of objects through membership predicates and to individually control the visibility of the instances in each group. Unlike previous smart visibility approaches, our approach controls the visibility on a per-instance basis and decides which instances are displayed or hidden based on the membership predicates and the current view. Thus, cluttered and dense volumes that are notoriously difficult to explore effectively are automatically sparsified so that the essential information is extracted and presented to the user. The proposed system is generic and can be easily integrated into existing volume rendering applications and applied to many different domains. We demonstrate the use of the volume conductor for visualizing fiber-reinforced polymers and intracellular organelle structures.

Abstract We present a combined volume and surface rendering technique with global illumination caching. Our approach uses volumetric path tracing to compute the global illumination volume and local shading models for rendering the isosurface. By joining both visualization approaches, we have enhanced the display and illumination of the surfaces while preserving physically realistic illumination of the participating media. To achieve real-time performance and avoid recomputing the image when the camera view changes, we compute the global illumination volume incrementally and defer the projection to a later step. We evaluated our technique by comparing different local shading models for isosurface rendering with the result of full volumetric path tracing and with the non-caching variant of our technique. Results show that the caching and non-caching variants perform comparably well, while the caching variant has the added benefit of being camera-view-independent. Additionally, we show that our approach emphasizes the surfaces within volumes better than volumetric path tracing.

Immersive virtual reality environments are gaining popularity for studying and exploring crowded three-dimensional structures. When reaching very high structural densities, the natural depiction of the scene produces impenetrable clutter and requires visibility and occlusion management strategies for exploration and orientation. Strategies developed to address the crowdedness in desktop applications, however, inhibit the feeling of immersion. They result in nonimmersive, desktop-style outside-in viewing in virtual reality. This article proposes Nanotilus-a new visibility and guidance approach for very dense environments that generates an endoscopic inside-out experience instead of outside-in viewing, preserving the immersive aspect of virtual reality. The approach consists of two novel, tightly coupled mechanisms that control scene sparsification simultaneously with camera path planning. The sparsification strategy is localized around the camera and is realized as a multi-scale, multi-shell, variety-preserving technique. When Nanotilus dives into the structures to capture internal details residing on multiple scales, it guides the camera using depth-based path planning. In addition to sparsification and path planning, we complete the tour generation with an animation controller, textual annotation, and text-to-visualization conversion. We demonstrate the generated guided tours on mesoscopic biological models - SARS-CoV-2 and HIV. We evaluate the Nanotilus experience with a baseline outside-in sparsification and navigational technique in a formal user study with 29 participants. While users can maintain a better overview using the outside-in sparsification, the study confirms our hypothesis that Nanotilus leads to stronger engagement and immersion.

Cryo-electron tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural details. Existing volume visualization methods, however, are not able to reveal details of interest due to low signal-to-noise ratio. In order to design more powerful transfer functions, we propose leveraging soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning, where we combine the advantages of two segmentation algorithms. First, the weak segmentation algorithm provides good results for propagating sparse user-provided labels to other voxels in the same volume and is used to generate dense pseudo-labels. Second, the powerful deep-learning-based segmentation algorithm learns from these pseudo-labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses deep-learning-based segmentation as a component for segmentation-aware transfer function design. Appropriate ramp parameters can be suggested automatically through frequency distribution analysis. Furthermore, our visualization uses gradient-free ambient occlusion shading to further suppress the visual presence of noise, and to give structural detail the desired prominence. The cryo-ET data studied in our technical experiments are based on the highest-quality tilted series of intact SARS-CoV-2 virions. Our technique shows the high impact in target sciences for visual data analysis of very noisy volumes that cannot be visualized with existing techniques.