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

MoSculp: Interactive Visualization of Shape and Time

We present a system that allows users to visualize complex human motion via 3D motion sculptures---a representation that conveys the 3D structure swept by a human body as it moves through space. Given an input video, our system computes the motion sculptures and provides a user interface for rendering it in different styles, including the options to insert the sculpture back into the original video, render it in a synthetic scene or physically print it. To provide this end-to-end workflow, we introduce an algorithm that estimates that human's 3D geometry over time from a set of 2D images and develop a 3D-aware image-based rendering approach that embeds the sculpture back into the scene. By automating the process, our system takes motion sculpture creation out of the realm of professional artists, and makes it applicable to a wide range of existing video material. By providing viewers with 3D information, motion sculptures reveal space-time motion information that is difficult to perceive with the naked eye, and allow viewers to interpret how different parts of the object interact over time. We validate the effectiveness of this approach with user studies, finding that our motion sculpture visualizations are significantly more informative about motion than existing stroboscopic and space-time visualization methods.Comment: UIST 2018. Project page: http://mosculp.csail.mit.edu

Layout of Multiple Views for Volume Visualization: A User Study

Abstract. Volume visualizations can have drastically different appearances when viewed using a variety of transfer functions. A problem then occurs in trying to organize many different views on one screen. We conducted a user study of four layout techniques for these multiple views. We timed participants as they separated different aspects of volume data for both time-invariant and time-variant data using one of four different layout schemes. The layout technique had no impact on performance when used with time-invariant data. With time-variant data, however, the multiple view layouts all resulted in better times than did a single view interface. Surprisingly, different layout techniques for multiple views resulted in no noticeable difference in user performance. In this paper, we describe our study and present the results, which could be used in the design of future volume visualization software to improve the productivity of the scientists who use it

Marine Heritage Monitoring with High Resolution Survey Tools: ScapaMAP 2001-2006

Archaeologically, marine sites can be just as significant as those on land. Until recently, however, they were not protected in the UK to the same degree, leading to degradation of sites; the difficulty of investigating such sites still makes it problematic and expensive to properly describe, schedule and monitor them. Use of conventional high-resolution survey tools in an archaeological context is changing the economic structure of such investigations however, and it is now possible to remotely but routinely monitor the state of submerged cultural artifacts. Use of such data to optimize expenditure of expensive and rare assets (e.g., divers and on-bottom dive time) is an added bonus. We present here the results of an investigation into methods for monitoring of marine heritage sites, using the remains of the Imperial German Navy (scuttled 1919) in Scapa Flow, Orkney as a case study. Using a baseline bathymetric survey in 2001 and a repeat bathymetric and volumetric survey in 2006, we illustrate the requirements for such surveys over and above normal hydrographic protocols and outline strategies for effective imaging of large wrecks. Suggested methods for manipulation of such data (including processing and visualization) are outlined, and we draw the distinction between products for scientific investigation and those for outreach and education, which have very different requirements. We then describe the use of backscatter and volumetric acoustic data in the investigation of wrecks, focusing on the extra information to be gained from them that is not evident in the traditional bathymetric DTM models or sounding point-cloud representations of data. Finally, we consider the utility of high-resolution survey as part of an integrated site management policy, with particular reference to the economics of marine heritage monitoring and preservation

Trends and concerns in digital cartography

CISRG discussion paper ;

Calipso: Physics-based Image and Video Editing through CAD Model Proxies

We present Calipso, an interactive method for editing images and videos in a physically-coherent manner. Our main idea is to realize physics-based manipulations by running a full physics simulation on proxy geometries given by non-rigidly aligned CAD models. Running these simulations allows us to apply new, unseen forces to move or deform selected objects, change physical parameters such as mass or elasticity, or even add entire new objects that interact with the rest of the underlying scene. In Calipso, the user makes edits directly in 3D; these edits are processed by the simulation and then transfered to the target 2D content using shape-to-image correspondences in a photo-realistic rendering process. To align the CAD models, we introduce an efficient CAD-to-image alignment procedure that jointly minimizes for rigid and non-rigid alignment while preserving the high-level structure of the input shape. Moreover, the user can choose to exploit image flow to estimate scene motion, producing coherent physical behavior with ambient dynamics. We demonstrate Calipso's physics-based editing on a wide range of examples producing myriad physical behavior while preserving geometric and visual consistency.Comment: 11 page