Real-Time Physically Based Deformation Using Transform Feedback

Movania, Muhammad Mobeen; Lin, Feng

doi:10.1201/b12288-21

Cited by 6 publications

(7 citation statements)

References 4 publications

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“…Movania and modified from an implementation presented in Refs. 21, 22. Figure 3 shows an overview diagram of our system.…”

Section: Design and Implementationmentioning

confidence: 99%

“…12–15 Advances in hardware acceleration and programmable GPU’s have made it easier to develop high-resolution multi-volume rendering, and numerous applications have been developed to take advantage of this., both commercial 16,17 and non-commercial. 18 Ray casting 19,20 is a common volume rendering technique 21,22 due to its high precision in visualizing the various medical images. 23 …”

Section: Introductionmentioning

confidence: 99%

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A stereoscopic system for viewing the temporal evolution of brain activity clusters in response to linguistic stimuli

et al. 2014

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In this paper, we present a novel application, 3D+Time Brain View, for the stereoscopic visualization of functional Magnetic Resonance Imaging (fMRI) data gathered from participants exposed to unfamiliar spoken languages. An analysis technique based on Independent Component Analysis (ICA) is used to identify statistically significant clusters of brain activity and their changes over time during different testing sessions. That is, our system illustrates the temporal evolution of participants’ brain activity as they are introduced to a foreign language through displaying these clusters as they change over time. The raw fMRI data is presented as a stereoscopic pair in an immersive environment utilizing passive stereo rendering. The clusters are presented using a ray casting technique for volume rendering. Our system incorporates the temporal information and the results of the ICA into the stereoscopic 3D rendering, making it easier for domain experts to explore and analyze the data.

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“…Movania and modified from an implementation presented in Refs. 21, 22. Figure 3 shows an overview diagram of our system.…”

Section: Design and Implementationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A stereoscopic system for viewing the temporal evolution of brain activity clusters in response to linguistic stimuli

et al. 2014

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“…With advances in fluorescence image acquisition and processing, such as confocal and Super Resolution Structured Illumination Microscopy (SR-SIM), it has become common practice to analyze the z-stacks, consisting of multiple two-dimensional (2D) fluorescence image frames, which these microscopes produce. These 2D images can be three-dimensionally (3D) reconstructed using direct-volume rendering [ 3 – 6 ], allowing the interrogation of the sample in 3D which can provide additional insight into biological events.…”

Section: Introductionmentioning

confidence: 99%

Improved region of interest selection and colocalization analysis in three-dimensional fluorescence microscopy samples using virtual reality

et al. 2018

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Although modern fluorescence microscopy produces detailed three-dimensional (3D) datasets, colocalization analysis and region of interest (ROI) selection is most commonly performed two-dimensionally (2D) using maximum intensity projections (MIP). However, these 2D projections exclude much of the available data. Furthermore, 2D ROI selections cannot adequately select complex 3D structures which may inadvertently lead to either the exclusion of relevant or the inclusion of irrelevant data points, consequently affecting the accuracy of the colocalization analysis. Using a virtual reality (VR) enabled system, we demonstrate that 3D visualization, sample interrogation and analysis can be achieved in a highly controlled and precise manner. We calculate several key colocalization metrics using both 2D and 3D derived super-resolved structured illumination-based data sets. Using a neuronal injury model, we investigate the change in colocalization between Tau and acetylated α-tubulin at control conditions, after 6 hours and again after 24 hours. We demonstrate that performing colocalization analysis in 3D enhances its sensitivity, leading to a greater number of statistically significant differences than could be established when using 2D methods. Moreover, by carefully delimiting the 3D structures under analysis using the 3D VR system, we were able to reveal a time dependent loss in colocalization between the Tau and microtubule network as an early event in neuronal injury. This behavior could not be reliably detected using a 2D based projection. We conclude that, using 3D colocalization analysis, biologically relevant samples can be interrogated and assessed with greater precision, thereby better exploiting the potential of fluorescence-based image analysis in biomedical research.

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“…These slices can also be defined arbitrarily, in the form of proxy geometry, which can be rendered instead of the image slices constituting the volume data. We aligned these slices with the viewer, where the proxy geometry is defined to be perpendicular to the viewing direction [ 7 , 8 ]. These proxy geometry slices are then rendered by the GPU in a back-to-front order, during which trilinear interpolation of the volume data is applied over the interior of the proxy geometry [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Virtual reality assisted microscopy data visualization and colocalization analysis

2017

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BackgroundConfocal microscopes deliver detailed three-dimensional data and are instrumental in biological analysis and research. Usually, this three-dimensional data is rendered as a projection onto a two-dimensional display. We describe a system for rendering such data using a modern virtual reality (VR) headset. Sample manipulation is possible by fully-immersive hand-tracking and also by means of a conventional gamepad. We apply this system to the specific task of colocalization analysis, an important analysis tool in biological microscopy. We evaluate our system by means of a set of user trials.ResultsThe user trials show that, despite inaccuracies which still plague the hand tracking, this is the most productive and intuitive interface. The inaccuracies nevertheless lead to a perception among users that productivity is low, resulting in a subjective preference for the gamepad. Fully-immersive manipulation was shown to be particularly effective when defining a region of interest (ROI) for colocalization analysis.ConclusionsVirtual reality offers an attractive and powerful means of visualization for microscopy data. Fully immersive interfaces using hand tracking show the highest levels of intuitiveness and consequent productivity. However, current inaccuracies in hand tracking performance still lead to a disproportionately critical user perception.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1446-2) contains supplementary material, which is available to authorized users.

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Real-Time Physically Based Deformation Using Transform Feedback

Cited by 6 publications

References 4 publications

A stereoscopic system for viewing the temporal evolution of brain activity clusters in response to linguistic stimuli

A stereoscopic system for viewing the temporal evolution of brain activity clusters in response to linguistic stimuli

Improved region of interest selection and colocalization analysis in three-dimensional fluorescence microscopy samples using virtual reality

Virtual reality assisted microscopy data visualization and colocalization analysis

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