. In Pacific Graphics 8-10 Oct. Seoul, Korea: Wiley & Sons Ltd. Abstract
This paper presents a technique to recover geometry from time-lapse sequences of outdoor scenes. We build upon photometric stereo techniques to recover approximate shadowing, shading and normal components allowing us to alter the material and normals of the scene. Previous work in analyzing such images has faced two fundamental difficulties: 1. the illumination in outdoor images consists of time-varying sunlight and skylight, and 2. the motion of the sun is restricted to a near-planar arc through the sky, making surface normal recovery unstable. We develop methods to estimate the reflection component due to skylight illumination. We also show that sunlight directions are usually non-planar, thus making surface normal recovery possible. This allows us to estimate approximate surface normals for outdoor scenes using a single day of data. We demonstrate the use of these surface normal for a number of image editing applications including reflectance, lighting, and normal editing.
. ACM Transactions on Graphics (Proc. SIGGRAPH), 33(6). Abstract
Separating a photograph into its reflectance and illumination intrinsicimages is a fundamentally ambiguous problem, and state-of-the-art algorithms combine sophisticated reflectance and illumination priors with user annotations to create plausible results. However, these algorithms cannot be easily extended to videos for two reasons: first, naıvely applying algorithms designed for single images to videos produce results that are temporally incoherent; second, effectively specifying user annotations for a video requires interactive feedback, and current approaches are orders of magnitudes too slow to support this. We introduce a fast and temporally consistent algorithm to decompose video sequences into their reflectance and illumination components. Our algorithm uses a hybrid formulation that separates image gradients into smooth illumination and sparse reflectance gradients using look-up tables. We use a multi-scale parallelized solver to reconstruct the reflectance and illumination from these gradients while enforcing spatial and temporal reflectance constraints and user annotations. We demonstrate that our algorithm automatically produces reasonable results, that can be interactively refined by users, at rates that are two orders of magnitude faster than existing tools, to produce high-quality decompositions for challenging real-world video sequences. We also show how these decompositions can be used for a number of video editing applications including recoloring, retexturing, illumination editing, and lighting-aware compositing.
The comprehensive analysis and characterization of cancer subtypes is an important problem to which significant resources have been devoted in recent years. In this paper we integrate the dual analysis method, which uses statistics to describe both the dimensions and the rows of a high dimensional dataset, into StratomeX, a Caleydo view tailored to cancer subtype analysis. We introduce significant difference plots for showing the elements of a candidate cancer subtype that differ significantly from other subtypes, thus enabling analysts to characterize cancer subtypes. We also enable analysts to investigate how samples relate to the subtype they are assigned and to the other groups. Our approach gives analysts the ability to create well-defined candidate subtypes based on statistical properties. We demonstrate the utility of our approach in three case studies, where we show that we are able to reproduce findings from a published cancer subtype characterization.
. IEEE Transactions on Visualization and Computer Graphics (VAST '14). Abstract
Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.
. IEEE Transactions on Visualization and Computer Graphics (InfoVis '14). Abstract
Answering questions about complex issues often requires analysts to take into account information contained in multiple interconnected datasets. A common strategy in analyzing and visualizing large and heterogeneous data is dividing it into meaningful subsets. Interesting subsets can then be selected and the associated data and the relationships between the subsets visualized. However, neither the extraction and manipulation nor the comparison of subsets is well supported by state-of-the-art techniques.
In this paper we present Domino, a novel multiform visualization technique for effectively representing subsets and the relationships between them. By providing comprehensive tools to arrange, combine, and extract subsets, Domino allows users to create both common visualization techniques and advanced visualizations tailored to specific use cases. In addition to the novel technique, we present an implementation that enables analysts to manage the wide range of options that our approach offers. Innovative interactive features such as placeholders and live previews support rapid creation of complex analysis setups. We introduce the technique and the implementation using a simple example and demonstrate scalability and effectiveness in a use case from the field of cancer genomics.
Cancer is a heterogeneous disease, and molecular profiling of tumors from large cohorts has enabled characterization of new tumor subtypes. This is a prerequisite for improving personalized treatment and ultimately achieving better patient outcomes. Potential tumor subtypes can be identified with methods such as unsupervised clustering or network-based stratification, which assign patients to sets based on high-dimensional molecular profiles. Detailed characterization of identified sets and their interpretation, however, remain a time-consuming exploratory process.
To address these challenges, we combined 'StratomeX', an interactive visualization tool that is freely available at http://www.caleydo.org/, with exploration tools to efficiently compare multiple patient stratifications, to correlate patient sets with clinical information or genomic alterations and to view the differences between molecular profiles across patient sets. Although we focus on cancer genomics here, StratomeX can also be applied in other disease cohorts.
BackgroundA complete understanding of the relationship between the amino acid sequence and resulting protein function remains an open problem in the biophysical sciences. Current approaches often rely on diagnosing functionally relevant mutations by determining whether an amino acid frequently occurs at a specific position within the protein family. However, these methods do not account for the biophysical properties and the 3D structure of the protein. We have developed an interactive visualization technique, Mu-8, that provides researchers with a holistic view of the differences of a selected protein with respect to a family of homologous proteins. Mu-8 helps to identify areas of the protein that exhibit: (1) significantly different bio-chemical characteristics, (2) relative conservation in the family, and (3) proximity to other regions that have suspect behavior in the folded protein.
MethodsOur approach quantifies and communicates the difference between a reference protein and its family based on amino acid indices or principal components of amino acid index classes, while accounting for conservation, proximity amongst residues, and overall 3D structure.
ResultsWe demonstrate Mu-8 in a case study with data provided by the 2013 BioVis contest. When comparing the sequence of a dysfunctional protein to its functional family, Mu-8 reveals several candidate regions that may cause function to break down.
. IEEE Transactions on Visualization and Computer Graphics (InfoVis '14). Abstract
Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.
. IEEE Transactions on Visualization and Computer Graphics, to appear. Abstract
We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.
Proofreading refers to the manual correction of automatic segmentations of image data. In connectomics, electron microscopy data is acquired at nanometer-scale resolution and results in very large image volumes of brain tissue that require fully automatic segmentation algorithms to identify cell boundaries. However, these algorithms require hundreds of corrections per cubic micron of tissue. Even though this task is time consuming, it is fairly easy for humans to perform corrections through splitting, merging, and adjusting segments during proofreading. In this paper we present the design and implementation of Mojo, a fully-featured single-user desktop application for proofreading, and Dojo, a multi-user web-based application for collaborative proofreading. We evaluate the accuracy and speed of Mojo, Dojo, and Raveler, a proofreading tool from Janelia Farm, through a quantitative user study. We designed a between-subjects experiment and asked non-experts to proofread neurons in a publicly available connectomics dataset. Our results show a significant improvement of corrections using web-based Dojo even in comparison to fully manual expert segmentation, when given the same amount of time. In addition, all participants using Dojo reported better usability. We discuss our findings and provide an analysis of requirements for designing visual proofreading software.
. Poster at the 4th Symposium on Biological Data Visualization. Abstract
We introduce NeuroLines, a novel tool designed for visualizing neuronal morphology and connectivity at the nanoscale level. NeuroLines uses a subway map metaphor to abstract the topology of 3D brain tissue data into a multi-scale, relative distance-preserving 2D visualization. This allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics attempts to reverse-engineer the wiring diagram of the brain. This task, coupled with the task of analyzing the detailed connectivity of neurites (axons, dendrites), is crucial to understanding the brain, its development and pathologies. However, the main challenge with such tasks is the enormous scale, complexity and visual clutter of nanoscale connectivity. This makes it difficult for existing visualization techniques to render such data in a meaningful way. NeuroLines offers a scalable visualization platform that can interactively render thousands of neurites in an uncluttered fashion, paired with interactive features to support the detail analysis of neuronal connectivity.
. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). Abstract
Most motion estimation algorithms (optical flow, layered models) cannot handle large amount of occlusion in textureless regions, as motion is often initialized with no occlusion assumption despite that occlusion may be included in the final objective. To handle such situations, we propose a local layering model where motion and occlusion relationships are inferred jointly. In particular, the uncertainties of occlusion relationships are retained so that motion is inferred by considering all the possibilities of local occlusion relationships. In addition, the local layering model handles articulated objects with self-occlusion. We demonstrate that the local layering model can handle motion and occlusion well for both challenging synthetic and real sequences.
. Eurographics Conference on Visualization (EuroVis), pp.to appear. Abstract
This survey gives an overview of the current state of the art in GPU techniques for interactive large-scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga-, tera-, and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out-of-core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e., output-sensitive algorithms and system designs. This leads to recent output-sensitive approaches that are ray-guided, visualization-driven, or display-aware. In this survey, we focus on these characteristics and propose a new categorization of GPU-based large-scale volume visualization techniques based on the notions of actual output-resolution visibility and the current working set of volume bricks - the current subset of data that is minimally required to produce an output image of the desired display resolution. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we discuss in this survey.
. Journal of Mathematical Imaging and Vision. Abstract
This article details two approaches to compute barycenters of measures using 1-D Wasserstein distances along radial projections of the input measures. The first method makes use of the Radon transform of the measures, and the second is the solution of a convex optimization problem over the space of measures. We show several properties of these barycenters and explain their relationship. We show numerical approximation schemes based on a discrete Radon transform and on the resolution of a non-convex optimization problem. We explore the respective merits and drawbacks of each approach on applications to two image processing problems: color transfer and texture mixing.
The facial performance of an individual is inherently rich in subtle deformation and timing details. Although these subtleties make the performance realistic and compelling, they often elude both motion capture and hand animation. We present a technique for adding fine-scale details and expressiveness to low-resolution art-directed facial performances, such as those created manually using a rig, via marker-based capture, by fitting a morphable model to a video, or through Kinect reconstruction using recent faceshift technology. We employ a high-resolution facial performance capture system to acquire a representative performance of an individual in which he or she explores the full range of facial expressiveness. From the captured data, our system extracts an expressiveness model that encodes subtle spatial and temporal deformation details specific to that particular individual. Once this model has been built, these details can be transferred to low-resolution artdirected performances. We demonstrate results on various forms of input; after our enhancement, the resulting animations exhibit the same nuances and fine spatial details as the captured performance, with optional temporal enhancement to match the dynamics of the actor. Finally, we show that our technique outperforms the current state-of-the-art in example-based facial animation.
We address the problem of segmenting an image into a previously unknown number of segments from the perspective of graph partitioning. Specifically, we consider minimum multicuts of superpixel affinity graphs in which all affinities between non-adjacent superpixels are negative. We propose a relaxation by Lagrangian decomposition and a constrained set of re-parameterizations for which we can optimize exactly and efficiently. Our contribution is to show how the planarity of the adjacency graph can be exploited if the affinity graph is non-planar. We demonstrate the effectiveness of this approach in user-assisted image segmentation and show that the solution of the relaxed problem is fast and the relaxation is tight in practice.
Abstract—Rankings are a popular and universal approach to structuring otherwise unorganized collections of items by computing a rank for each item based on the value of one or more of its attributes. This allows us, for example, to prioritize tasks or to evaluate the performance of products relative to each other. While the visualization of a ranking itself is straightforward, its interpretation is not, because the rank of an item represents only a summary of a potentially complicated relationship between its attributes and those of the other items. It is also common that alternative rankings exist which need to be compared and analyzed to gain insight into how multiple heterogeneous attributes affect the rankings. Advanced visual exploration tools are needed to make this process efficient. In this paper we present a comprehensive analysis of requirements for the visualization of multi-attribute rankings. Based on these considerations, we propose LineUp-a novel and scalable visualization technique that uses bar charts. This interactive technique supports the ranking of items based on multiple heterogeneous attributes with different scales and semantics. It enables users to interactively combine attributes and flexibly refine parameters to explore the effect of changes in the attribute combination. This process can be employed to derive actionable insights as to which attributes of an item need to be modified in order for its rank to change. Additionally, through integration of slope graphs, LineUp can also be used to compare multiple alternative rankings on the same set of items, for example, over time or across different attribute combinations. We evaluate the effectiveness of the proposed multi-attribute visualization technique in a qualitative study. The study shows that users are able to successfully solve complex ranking tasks in a short period of time.
Recent advances in high-resolution microscopy allow neuroscientists to acquire volume data of neural tissue of extreme size. However, the tremendous resolution and the high complexity of neural structures present big challenges to storage, processing, and visualization at interactive rates. We present a system for interactive exploration of petascale (petavoxel) volumes resulting from high-throughput electron microscopy data streams. Our system can concurrently handle multiple volumes, and also supports the simultaneous visualization of high-resolution voxel segmentation data. We employ a visualization-driven system design that allows us to restrict most computations to a small sub-set of the data. We employ a multi-resolution virtual memory architecture for better scalability than previous approaches and handling of incomplete data. We illustrate the real-world use of our system for a mouse cortex volume of one teravoxel in size, where several hundred neurites as well as synapses have been segmented and labeled.
This paper presents ConnectomeExplorer, an application for the interactive exploration and query-guided visual analysis of large volumetric electron microscopy (EM) data sets in connectomics research. Our system incorporates a knowledge-based query algebra that supports the interactive specification of dynamically evaluated queries, which enable neuroscientists to pose and answer domain-specific questions in an intuitive manner. Queries are built step by step in a visual query builder, building more complex queries from combinations of simpler queries. Our application is based on a scalable volume visualization framework that scales to multiple volumes of several teravoxels each, enabling the concurrent visualization and querying of the original EM volume, additional segmentation volumes, neuronal connectivity, and additional meta data comprising a variety of neuronal data attributes. We evaluate our application on a data set of roughly one terabyte of EM data and 750 GB of segmentation data, containing over 4,000 segmented structures and 1,000 synapses. We demonstrate typical use-case scenarios of our collaborators in neuroscience, where our system has enabled them to answer specific scientific questions using interactive querying and analysis on the full-size data for the first time.