Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

Semantic multimedia remote display for mobile thin clients

Current remote display technologies for mobile thin clients convert practically all types of graphical content into sequences of images rendered by the client. Consequently, important information concerning the content semantics is lost. The present paper goes beyond this bottleneck by developing a semantic multimedia remote display. The principle consists of representing the graphical content as a real-time interactive multimedia scene graph. The underlying architecture features novel components for scene-graph creation and management, as well as for user interactivity handling. The experimental setup considers the Linux X windows system and BiFS/LASeR multimedia scene technologies on the server and client sides, respectively. The implemented solution was benchmarked against currently deployed solutions (VNC and Microsoft-RDP), by considering text editing and WWW browsing applications. The quantitative assessments demonstrate: (1) visual quality expressed by seven objective metrics, e.g., PSNR values between 30 and 42 dB or SSIM values larger than 0.9999; (2) downlink bandwidth gain factors ranging from 2 to 60; (3) real-time user event management expressed by network round-trip time reduction by factors of 4-6 and by uplink bandwidth gain factors from 3 to 10; (4) feasible CPU activity, larger than in the RDP case but reduced by a factor of 1.5 with respect to the VNC-HEXTILE

Inviwo -- A Visualization System with Usage Abstraction Levels

The complexity of today's visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities

Progressive refinement rendering of implicit surfaces

The visualisation of implicit surfaces can be an inefficient task when such surfaces are complex and highly detailed. Visualising a surface by first converting it to a polygon mesh may lead to an excessive polygon count. Visualising a surface by direct ray casting is often a slow procedure. In this paper we present a progressive refinement renderer for implicit surfaces that are Lipschitz continuous. The renderer first displays a low resolution estimate of what the final image is going to be and, as the computation progresses, increases the quality of this estimate at an interactive frame rate. This renderer provides a quick previewing facility that significantly reduces the design cycle of a new and complex implicit surface. The renderer is also capable of completing an image faster than a conventional implicit surface rendering algorithm based on ray casting

Real-time Cinematic Design Of Visual Aspects In Computer-generated Images

Creation of visually-pleasing images has always been one of the main goals of computer graphics. Two important components are necessary to achieve this goal --- artists who design visual aspects of an image (such as materials or lighting) and sophisticated algorithms that render the image. Traditionally, rendering has been of greater interest to researchers, while the design part has always been deemed as secondary. This has led to many inefficiencies, as artists, in order to create a stunning image, are often forced to resort to the traditional, creativity-baring, pipelines consisting of repeated rendering and parameter tweaking. Our work shifts the attention away from the rendering problem and focuses on the design. We propose to combine non-physical editing with real-time feedback and provide artists with efficient ways of designing complex visual aspects such as global illumination or all-frequency shadows. We conform to existing pipelines by inserting our editing components into existing stages, hereby making editing of visual aspects an inherent part of the design process. Many of the examples showed in this work have been, until now, extremely hard to achieve. The non-physical aspect of our work enables artists to express themselves in more creative ways, not limited by the physical parameters of current renderers. Real-time feedback allows artists to immediately see the effects of applied modifications and compatibility with existing workflows enables easy integration of our algorithms into production pipelines

Interactive visualization tool for multi-channel confocal microscopy data in neurobiology research

Journal ArticleConfocal microscopy is widely used in neurobiology for studying the three-dimensional structure of the nervous system. Confocal image data are often multi-channel, with each channel resulting from a different fluorescent dye or fluorescent protein; one channel may have dense data, while another has sparse; and there are often structures at several spatial scales: subneuronal domains, neurons, and large groups of neurons (brain regions). Even qualitative analysis can therefore require visualization using techniques and parameters fine-tuned to a particular dataset. Despite the plethora of volume rendering techniques that have been available for many years, the techniques standardly used in neurobiological research are somewhat rudimentary, such as looking at image slices or maximal intensity projections. Thus there is a real demand from neurobiologists, and biologists in general, for a flexible visualization tool that allows interactive visualization of multi-channel confocal data, with rapid fine-tuning of parameters to reveal the three dimensional relationships of structures of interest. Together with neurobiologists, we have designed such a tool, choosing visualization methods to suit the characteristics of confocal data and a typical biologist's workflow. We use interactive volume rendering with intuitive settings for multidimensional transfer functions, multiple render modes and multi-views for multi-channel volume data, and embedding of polygon data into volume data for rendering and editing. As an example, we apply this tool to visualize confocal microscopy datasets of the developing zebrafish visual system