Cytosplore: Interactive Immune Cell Phenotyping for Large Single‐Cell Datasets

To understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells' corresponding properties and functionality. Mass cytometry is a novel technique to determine the properties of single‐cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis. In this work, we present Cytosplore, implementing an interactive workflow to analyze mass cytometry data in an integrated system, providing multiple linked views, showing different levels of detail and enabling the rapid definition of known and unknown cell types. Cytosplore handles millions of cells, each represented as a high‐dimensional data point, facilitates hypothesis generation and confirmation, and provides a significant speed up of the current workflow. We show the effectiveness of Cytosplore in a case study evaluation.     

Generalized As‐Similar‐As‐Possible Warping with Applications in Digital Photography

Discrete conformal mappings of planar triangle meshes, also known as the As‐Similar‐As‐Possible (ASAP) mapping, involve the minimization of a quadratic energy function, thus are very easy to generate and are popular in image warping scenarios. We generalize this classical mapping to the case of quad meshes, taking into account the mapping of the interior of the quad, and analyze in detail the most common case ‐ the unit grid mesh. We show that the generalization, when combined with barycentric coordinate mappings between the source and target polygons, spawns an entire family of new mappings governed by quadratic energy functions, which allow to control quite precisely various effects of the mapping. This approach is quite general and applies also to arbitrary planar polygon meshes. As an application of generalized ASAP mappings of the unit grid mesh, we demonstrate how they can be used to warp digital photographs to achieve a variety of effects. One such effect is modifying the perspective of the camera that took a given photograph (without moving the camera). A related, but more challenging, effect is re‐photography ‐ warping a contemporary photograph in order to reproduce the camera view present in a vintage photograph of the same scene ‐ taken many years before with a different camera from a different viewpoint. We apply the generalized ASAP mapping to these images, discretized to a unit grid. Using a quad mesh (as opposed to a triangle mesh) permits biasing towards affine maps of the unit squares. This allows the introduction of an As‐Affine‐As‐Possible (AAAP) mapping for a good approximation of the homographies present in these warps, achieving quite accurate results. We demonstrate the advantages of the AAAP mapping on a variety of synthetic and real‐world examples.     

MIQP‐based Layout Design for Building Interiors

We propose a hierarchical framework for the generation of building interiors. Our solution is based on a mixed integer quadratic programming (MIQP) formulation. We parametrize a layout by polygons that are further decomposed into small rectangles. We identify important high‐level constraints, such as room size, room position, room adjacency, and the outline of the building, and formulate them in a way that is compatible with MIQP and the problem parametrization. We also propose a hierarchical framework to improve the scalability of the approach. We demonstrate that our algorithm can be used for residential building layouts and can be scaled up to large layouts such as office buildings, shopping malls, and supermarkets. We show that our method is faster by multiple orders of magnitude than previous methods.     

InSpectr: Multi‐Modal Exploration,Visualization, and Analysis of Spectral Data

This paper addresses the increasing demand in industry for methods to analyze and visualize multimodal data involving a spectral modality. Two data modalities are used: high‐resolution X‐ray computed tomography (XCT) for structural characterization and low‐resolution X‐ray fluorescence (XRF) spectral data for elemental decomposition. We present InSpectr, an integrated tool for the interactive exploration and visual analysis of multimodal, multiscalar data. The tool has been designed around a set of tasks identified by domain experts in the fields of XCT and XRF. It supports registered single scalar and spectral datasets optionally coupled with element maps and reference spectra. InSpectr is instantiating various linked views for the integration of spatial and non‐spatial information to provide insight into an industrial component's structural and material composition: views with volume renderings of composite and individual 3D element maps visualize global material composition; transfer functions defined directly on the spectral data and overlaid pie‐chart glyphs show elemental composition in 2D slice‐views; a representative aggregated spectrum and spectra density histograms are introduced to provide a global overview in the spectral view. Spectral magic lenses, spectrum probing and elemental composition probing of points using a pie‐chart view and a periodic table view aid the local material composition analysis. Two datasets are investigated to outline the usefulness of the presented techniques: a 3D virtually created phantom with a brass metal alloy and a real‐world 2D water phantom with insertions of gold, barium, and gadolinium. Additionally a detailed user evaluation of the results is provided.     

Clean color: Improving multi‐filament 3D prints

Fused Filament Fabrication is an additive manufacturing process by which a 3D object is created from plastic filament. The filament is pushed through a hot nozzle where it melts. The nozzle deposits plastic layer after layer to create the final object. This process has been popularized by the RepRap community. Several printers feature multiple extruders, allowing objects to be formed from multiple materials or colors. The extruders are mounted side by side on the printer carriage. However, the print quality suffers when objects with color patterns are printed – a disappointment for designers interested in 3D printing their colored digital models. The most severe issue is the oozing of plastic from the idle extruders: Plastics of different colors bleed onto each other giving the surface a smudged aspect, excess strings oozing from the extruder deposit on the surface, and holes appear due to this missing plastic. Fixing this issue is difficult: increasing the printing speed reduces oozing but also degrades surface quality – on large prints the required speed level become impractical. Adding a physical mechanism increases cost and print time as extruders travel to a cleaning station. Instead, we rely on software and exploit degrees of freedom of the printing process. We introduce three techniques that complement each other in improving the print quality significantly. We first reduce the impact of oozing plastic by choosing a better azimuth angle for the printed part. We build a disposable rampart in close proximity of the part, giving the extruders the opportunity to wipe oozing strings and refill with hot plastic. We finally introduce a toolpath planner avoiding and hiding most of the defects due to oozing, and seamlessly integrating the rampart. We demonstrate our technique on several challenging multiple color prints, and show that our tool path planner improves the surface finish of single color prints as well.     

Visualizing Probabilistic Multi‐Phase Fluid Simulation Data using a Sampling Approach

Eulerian Method of Moment (MoM) solvers are gaining popularity for multi‐phase CFD simulation involving bubbles or droplets in process engineering. Because the actual positions of bubbles are uncertain, the spatial distribution of bubbles is described by scalar fields of moments, which can be interpreted as probability density functions. Visualizing these simulation results and comparing them to physical experiments is challenging, because neither the shape nor the distribution of bubbles described by the moments lend themselves to visual interpretation. In this work, we describe a visualization approach that provides explicit instances of the bubble distribution and produces bubble geometry based on local flow properties. To facilitate animation, the instancing of the bubble distribution provides coherence over time by advancing bubbles between time steps and updating the distribution. Our approach provides an intuitive visualization and enables direct visual comparison of simulation results to physical experiments.     

Visual and quantitative analysis of great arteries’ blood flow jets in cardiac 4D PC‐MRI data

Flow in the great arteries (aorta, pulmonary artery) is normally laminar with a parabolic velocity profile. Eccentric flow jets are linked to various diseases like aneurysms. Cardiac 4D PC‐MRI data provide spatio‐temporally resolved blood flow information for the whole cardiac cycle. In this work, we establish a time‐dependent visualization and quantification of flow jets. For this purpose, equidistant measuring planes are automatically placed along the vessel's centerline. The flow jet position and region with highest velocities are extracted for every plane in each time step. This is done during pre‐processing and without user‐defined parameters. We visualize the main flow jet as geometric tube. High‐velocity areas are depicted as a net around this tube. Both geometries are time‐dependent and can be animated. Quantitative values are provided during cross‐sectional measuring plane‐based evaluation. Moreover, we offer a plot visualization as summary of flow jet characteristics for the selected plane. Our physiologically plausible results are in accordance with medical findings. Our clinical collaborators appreciate the possibility to view the flow jet in the whole vessel at once, which normally requires repeated pathline filtering due to varying velocities along the vessel course. The overview plots are considered as valuable for documentation purposes.     

Semi‐automatic Vortex Flow Classification in 4D PC‐MRI Data of the Aorta

We present an Aortic Vortex Classification (AVOCLA) that allows to classify vortices in the human aorta semi‐automatically. Current medical studies assume a strong relation between cardiovascular diseases and blood flow patterns such as vortices. Such vortices are extracted and manually classified according to specific, unstandardized properties. We employ an agglomerative hierarchical clustering to group vortex‐representing path lines as basis for the subsequent classification. Classes are based on the vortex' size, orientation and shape, its temporal occurrence relative to the cardiac cycle as well as its spatial position relative to the vessel course. The classification results are presented by a 2D and 3D visualization technique. To confirm the usefulness of both approaches, we report on the results of a user study. Moreover, AVOCLA was applied to 15 datasets of healthy volunteers and patients with different cardiovascular diseases. The results of the semi‐automatic classification were qualitatively compared to a manually generated ground truth of two domain experts considering the vortex number and five specific properties.     

Glyphs for Asymmetric Second‐Order 2D Tensors

Tensors model a wide range of physical phenomena. While symmetric tensors are sufficient for some applications (such as diffusion), asymmetric tensors are required, for example, to describe differential properties of fluid flow. Glyphs permit inspecting individual tensor values, but existing tensor glyphs are fully defined only for symmetric tensors. We propose a glyph to visualize asymmetric second‐order two‐dimensional tensors. The glyph includes visual encoding for physically significant attributes of the tensor, including rotation, anisotropic stretching, and isotropic dilation. Our glyph design conserves the symmetry and continuity properties of the underlying tensor, in that transformations of a tensor (such as rotation or negation) correspond to analogous transformations of the glyph. We show results with synthetic data from computational fluid dynamics.     

An Interactive Design System of Free‐Formed Bamboo‐Copters

We present an interactive design system for designing free‐formed bamboo‐copters, where novices can easily design free‐formed, even asymmetric bamboo‐copters that successfully fly. The designed bamboo‐copters can be fabricated using digital fabrication equipment, such as a laser cutter. Our system provides two useful functions for facilitating this design activity. First, it visualizes a simulated flight trajectory of the current bamboo‐copter design, which is updated in real time during the user's editing. Second, it provides an optimization function that automatically tweaks the current bamboo‐copter design such that the spin quality—how stably it spins—and the flight quality—how high and long it flies—are enhanced. To enable these functions, we present non‐trivial extensions over existing techniques for designing free‐formed model airplanes [ UKSI14 ], including a wing discretization method tailored to free‐formed bamboo‐copters and an optimization scheme for achieving stable bamboo‐copters considering both spin and flight qualities.     

Interactive Image‐Guided Modeling of Extruded Shapes

A recent trend in interactive modeling of 3D shapes from a single image is designing minimal interfaces, and accompanying algorithms, for modeling a specific class of objects. Expanding upon the range of shapes that existing minimal interfaces can model, we present an interactive image‐guided tool for modeling shapes made up of extruded parts. An extruded part is represented by extruding a closed planar curve, called base, in the direction orthogonal to the base. To model each extruded part, the user only needs to sketch the projected base shape in the image. The main technical contribution is a novel optimization‐based approach for recovering the 3D normal of the base of an extruded object by exploring both geometric regularity of the sketched curve and image contents. We developed a convenient interface for modeling multi‐part shapes and a method for optimizing the relative placement of the parts. Our tool is validated using synthetic data and tested on real‐world images.     

The shape variational autoencoder: A deep generative model of part‐segmented 3D objects

We introduce a generative model of part‐segmented 3D objects: the shape variational auto‐encoder (ShapeVAE). The ShapeVAE describes a joint distribution over the existence of object parts, the locations of a dense set of surface points, and over surface normals associated with these points. Our model makes use of a deep encoder‐decoder architecture that leverages the part‐decomposability of 3D objects to embed high‐dimensional shape representations and sample novel instances. Given an input collection of part‐segmented objects with dense point correspondences the ShapeVAE is capable of synthesizing novel, realistic shapes, and by performing conditional inference enables imputation of missing parts or surface normals. In addition, by generating both points and surface normals, our model allows for the use of powerful surface‐reconstruction methods for mesh synthesis. We provide a quantitative evaluation of the ShapeVAE on shape‐completion and test‐set log‐likelihood tasks and demonstrate that the model performs favourably against strong baselines. We demonstrate qualitatively that the ShapeVAE produces plausible shape samples, and that it captures a semantically meaningful shape‐embedding. In addition we show that the ShapeVAE facilitates mesh reconstruction by sampling consistent surface normals.     

User‐Assisted Video Stabilization

We present a user‐assisted video stabilization algorithm that is able to stabilize challenging videos when state‐of‐the‐art automatic algorithms fail to generate a satisfactory result. Current methods do not give the user any control over the look of the final result. Users either have to accept the stabilized result as is, or discard it should the stabilization fail to generate a smooth output. Our system introduces two new modes of interaction that allow the user to improve the unsatisfactory stabilized video. First, we cluster tracks and visualize them on the warped video. The user ensures that appropriate tracks are selected by clicking on track clusters to include or exclude them. Second, the user can directly specify how regions in the output video should look by drawing quadrilaterals to select and deform parts of the frame. These user‐provided deformations reduce undesirable distortions in the video. Our algorithm then computes a stabilized video using the user‐selected tracks, while respecting the user‐modified regions. The process of interactively removing user‐identified artifacts can sometimes introduce new ones, though in most cases there is a net improvement. We demonstrate the effectiveness of our system with a variety of challenging hand held videos.     

Learning 3D Scene Synthesis from Annotated RGB‐D Images

We present a data‐driven method for synthesizing 3D indoor scenes by inserting objects progressively into an initial, possibly, empty scene. Instead of relying on few hundreds of hand‐crafted 3D scenes, we take advantage of existing large‐scale annotated RGB‐D datasets, in particular, the SUN RGB‐D database consisting of 10,000+ depth images of real scenes, to form the prior knowledge for our synthesis task. Our object insertion scheme follows a co‐occurrence model and an arrangement model, both learned from the SUN dataset. The former elects a highly probable combination of object categories along with the number of instances per category while a plausible placement is defined by the latter model. Compared to previous works on probabilistic learning for object placement, we make two contributions. First, we learn various classes of higher‐order object‐object relations including symmetry, distinct orientation, and proximity from the database. These relations effectively enable considering objects in semantically formed groups rather than by individuals. Second, while our algorithm inserts objects one at a time, it attains holistic plausibility of the whole current scene while offering controllability through progressive synthesis. We conducted several user studies to compare our scene synthesis performance to results obtained by manual synthesis, state‐of‐the‐art object placement schemes, and variations of parameter settings for the arrangement model.     

Visual Analysis of Governing Topological Structures in Excitable Network Dynamics

To understand how topology shapes the dynamics in excitable networks is one of the fundamental problems in network science when applied to computational systems biology and neuroscience. Recent advances in the field discovered the influential role of two macroscopic topological structures, namely hubs and modules. We propose a visual analytics approach that allows for a systematic exploration of the role of those macroscopic topological structures on the dynamics in excitable networks. Dynamical patterns are discovered using the dynamical features of excitation ratio and co‐activation. Our approach is based on the interactive analysis of the correlation of topological and dynamical features using coordinated views. We designed suitable visual encodings for both the topological and the dynamical features. A degree map and an adjacency matrix visualization allow for the interaction with hubs and modules, respectively. A barycentric‐coordinates layout and a multi‐dimensional scaling approach allow for the analysis of excitation ratio and co‐activation, respectively. We demonstrate how the interplay of the visual encodings allows us to quickly reconstruct recent findings in the field within an interactive analysis and even discovered new patterns. We apply our approach to network models of commonly investigated topologies as well as to the structural networks representing the connectomes of different species. We evaluate our approach with domain experts in terms of its intuitiveness, expressiveness, and usefulness.     

AutoStyle: Automatic Style Transfer from Image Collections to Users' Images

Stylizing photos, to give them an antique or artistic look, has become popular in recent years. The available stylization filters, however, are usually created manually by artists, resulting in a narrow set of choices. Moreover, it can be difficult for the user to select a desired filter, since the filters’ names often do not convey their functions. We investigate an approach to photo filtering in which the user provides one or more keywords, and the desired style is defined by the set of images returned by searching the web for those keywords. Our method clusters the returned images, allows the user to select a cluster, then stylizes the user's photos by transferring vignetting, color, and local contrast from that cluster. This approach vastly expands the range of available styles, and gives each filter a meaningful name by default. We demonstrate that our method is able to robustly transfer a wide range of styles from image collections to users’ photos.