RSS 1.0KAUST Visualization Laboratory (KVL)
The Visualization Laboratory at KAUST is a fully staffed state-of-the-art facility that offers students, faculty, researchers and university collaborators a unique opportunity to utilize one-of-a-kind visualization, interaction, and computational resources for the exploration and presentation of scientific data. 2D and 3D display environments, highly spatialized and immersive audio, monoscopic and stereoscopic displays, wireless interaction devices, and fully integrated and portable desktop applications are some of the services the laboratory offers. All spaces are fully interconnected with a 10Gb link, and can also be utilized for academic events and research meetings. Audio/video streaming, recording, and playback of research presentations/seminars are available throughout the facility. The facility is available for use by any KAUST member, and the laboratory staff can provide assistance in creating new customized applications with their expertise in computer graphics, human-computer interaction, virtual reality, scientific visualization and sonification. A Special Research Partnership has also been established between KAUST and the CalIT2 Institute at University of California San Diego. The design and implementation of the lab facilities was done in collaboration with UCSD and new research projects can avail the full benefit of this ongoing partnership. Students from KAUST academic programs spend summer internships at UCSD, collaborating with research scientists there and coming back to the lab to apply and implement their newly learned skills. Contact us at vislab@kaust.edu.sa
Recent Submissions
-
Improving classification of correct and incorrect protein-protein docking models by augmenting the training set(Bioinformatics Advances, Oxford University Press (OUP), 2023-02-02) [Article]Motivation: Protein-protein interactions drive many relevant biological events, such as infection, replication, and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D structures. However, such experiments take time and are expensive; moreover, the current technology cannot keep up with the high discovery rate of new interactions. Computational modeling, like protein-protein docking, can help to fill this gap by generating docking poses. Protein-protein docking generally consists of two parts, sampling and scoring. The sampling is an exhaustive search of the tridimensional space. The caveat of the sampling is that it generates a large number of incorrect poses, producing a highly unbalanced dataset. This limits the utility of the data to train machine learning classifiers. Results: Using weak supervision, we developed a data augmentation method that we named hAIkal. Using hAIkal, we increased the labeled training data to train several algorithms. We trained and obtained different classifiers; the best classifier has 81% accuracy and 0.51 MCC on the test set, surpassing the state-of-the-art scoring functions.
-
Riemannian Geometry for Scientific Visualization(ACM, 2023-01-31) [Conference Paper]This tutorial introduces the most important basics of Riemannian geometry and related concepts with a specific focus on applications in scientific visualization. The main concept in Riemannian geometry is the presence of a Riemannian metric on a differentiable manifold, comprising a second-order tensor field that defines an inner product in each tangent space that varies smoothly from point to point. Technically, the metric is what allows defining and computing distances and angles in a coordinate-independent manner. However, even more importantly, it in a sense is really the major structure (on top of topological considerations) that defines the space where scientific data, such as scalar, vector, and tensor fields live.
-
Imaging Oil Recovery from Mixed-Wet Microporous Carbonates(Society of Exploration Geophysicists and American Association of Petroleum Geologists, 2022-08-15) [Conference Paper]This paper summarizes some of our efforts in comprehensive imaging of a complex limestone-water-asphaltenic crude oil reservoir system at scales ranging from a fraction of a micron to centimeters. These types of imaging and analyses that follow are necessary if one were to understand fully the fundamentals of improved oil recovery in mixed wet rock. Perhaps as much as 50% of the oil-in-place in carbonate formations around the world is locked away in the easy to bypass microporosity. If some of this oil is unlocked by the improved recovery processes designed speci cally for tight carbonate formations, the world may gain a major source of lower-rate power over several decades. Here, we overview our work on the Arab D limestones and Indiana limestones. We investigate the occurrence of microporosity of different origins and sizes using scanning electron microscopy (SEM) and pore casting techniques. We show that large portions of the micropores in Arab D formation would have been bypassed during primary drainage unless the invading crude oil ganglia were su ciently long. We also show that, under prevailing conditions of primary drainage of the strongly water-wet Arab formations in the Ghawar, the microporosity there was invaded and the porosity-weighted initial oil saturations of 60-85% are expected. Considering the asphaltenic nature of crude oil in the Ghawar, we expect the invaded portions of the pores to turn mixed-wet, thus becoming inaccessible to water ooding until further measures are taken to modify the system's surface chemistry and/or create substantial local pore pressure gradients. All types of imaging and experiments described in this paper guide our spontaneous counter-current imbibition in Amott cell experiments, a convenient laboratory method of studying oil recovery from oil-saturated rock samples in secondary or tertiary oil recovery by water ood of tunable composition. Classical Amott cell experiment estimates ultimate oil recovery. It is not designed, however, for studying the dynamics of oil recovery. In this work we identify and x a aw in the classical Amott cell imbibition experiments that hinders the development of predictive recovery models for mixed-wet carbonates. We then follow with a statistical analysis and scaling of the imbibition. We apply Generalized Extreme Value distribution to model the cumulative oil production. Here, we start with the Amott imbibition experiments and scaling analysis for Indiana limestone core plugs saturated with mineral oil. The knowledge gained from this study will allow us to develop a predictive model of water-oil displacement for reservoir carbonate rock and crude oil recovery systems.
-
Sonification of Animal Tracks as an Alternative Representation of Multi-Dimensional Data: A Northern Elephant Seal Example(Frontiers in Marine Science, Frontiers Media SA, 2018-04-20) [Article]Understanding movement of marine megafauna across the ocean is largely based on approaches and models based on analysis of tracks of single animals. While this has led to major progress, the possibility of concerted group dynamics has not been sufficiently examined, possibly due to challenges in exploring massive amounts of data required to this end. Here we report a sonification experiment, where the collective movement of northern elephant seals (Mirounga angustirostris) was explored by coding their group dynamics into sound. Specifically, we converted into sound data derived from a tagging program involving a total of 321 tagged animals tracked over a decade, between 20 February 2004 and 30 May 2014, consisting of an observation period of 90,063 h, composed of 1,027,839 individual positions. The data parameters used to provide the sound are position (longitude) and spread (degree of displacement taken for the active group). These data parameters are mapped to the sonic parameters of frequency (pitch) and amplitude (volume), respectively. Examination of the resulting sound revealed features of motion that translate into specific patterns in space. The serial departure of elephant seals to initiate their trips into waves is clearly reflected in the addition of tonalities, with coherent swimming of the animals conforming a wave reflected in the modulated fluctuations in volume, suggesting coordinated fluctuations in dispersion of the wave. Smooth changes in volume, coordinated with pitch variability, indicate that the animals spread out as they move further away from the colony, with one or a few animals exploring an ocean area away from that explored by the core wave. The shift in volume and pitch also signals at group coordination in initiating the return home. Coordinated initiation of the return to the colony is also clearly revealed by the sonification, as reflected in an increase in volume and pitch of the notes denoting the movement of each animal in a migration wave. This sonification reveals clear patterns of covariation in movement data, which drivers and triggers, whether intrinsic or environmental, cannot be elucidated here but allow to formulate a number of non-trivial questions on the synchronized nature of group behavior of northern elephant seals foraging across the NE Pacific Ocean.
-
Modeling and Analysis of Magnetic Nanoparticles Injection in Water-Oil Two-Phase Flow in Porous Media under Magnetic Field Effect(Geofluids, Hindawi Limited, 2017-08-28) [Article]In this paper, the magnetic nanoparticles are injected into a water-oil, two-phase system under the influence of an external permanent magnetic field. We lay down the mathematical model and provide a set of numerical exercises of hypothetical cases to show how an external magnetic field can influence the transport of nanoparticles in the proposed two-phase system in porous media. We treat the water-nanoparticles suspension as a miscible mixture, whereas it is immiscible with the oil phase. The magnetization properties, the density, and the viscosity of the ferrofluids are obtained based on mixture theory relationships. In the mathematical model, the phase pressure contains additional term to account for the extra pressures due to fluid magnetization effect and the magnetostrictive effect. As a proof of concept, the proposed model is applied on a countercurrent imbibition flow system in which both the displacing and the displaced fluids move in opposite directions. Physical variables, including waternanoparticles suspension saturation, nanoparticles concentration, and pore wall/throat concentrations of deposited nanoparticles, are investigated under the influence of the magnetic field. Two different locations of the magnet are studied numerically, and variations in permeability and porosity are considered.
-
Adding large EM stack support(2016 4th Saudi International Conference on Information Technology (Big Data Analysis) (KACSTIT), Institute of Electrical and Electronics Engineers (IEEE), 2016-12-01) [Conference Paper]Serial section electron microscopy (SSEM) image stacks generated using high throughput microscopy techniques are an integral tool for investigating brain connectivity and cell morphology. FIB or 3View scanning electron microscopes easily generate gigabytes of data. In order to produce analyzable 3D dataset from the imaged volumes, efficient and reliable image segmentation is crucial. Classical manual approaches to segmentation are time consuming and labour intensive. Semiautomatic seeded watershed segmentation algorithms, such as those implemented by ilastik image processing software, are a very powerful alternative, substantially speeding up segmentation times. We have used ilastik effectively for small EM stacks – on a laptop, no less; however, ilastik was unable to carve the large EM stacks we needed to segment because its memory requirements grew too large – even for the biggest workstations we had available. For this reason, we refactored the carving module of ilastik to scale it up to large EM stacks on large workstations, and tested its efficiency. We modified the carving module, building on existing blockwise processing functionality to process data in manageable chunks that can fit within RAM (main memory). We review this refactoring work, highlighting the software architecture, design choices, modifications, and issues encountered.
-
Simulation and visualization of the cyclonic storm chapala over the arabian sea: a case study(2016 4th Saudi International Conference on Information Technology (Big Data Analysis) (KACSTIT), Institute of Electrical and Electronics Engineers (IEEE), 2016-12-01) [Conference Paper]We use the high resolution Weather Research and Forecasting (WRF) model to predict the characteristics of an intense cyclone, Chapala, which formed over the Arabian Sea in October/November 2015. The implemented model consists of two-way interactive nested domains of 9 and 3km. The prediction experiment of the cyclone started on 1200UTC of 26 October 2015 to forecast its landfall and its intensity based on NCEP global model forecasting fields. The results show that the movement of Chapala is well reproduced by our model up to 72 hours, after which track errors become significant. The intensity and cloud features of the extreme event as well as the distribution of hydrometeors is well represented by the model. All the characteristics including eye and eye-wall regions, mesoscale convective systems and distribution of different hydrometers during the lifetime of Chapala are very well simulated. The model output results in several hundred gigabytes of data, we analyze and visualize these data using state of the art computational and visualization software for representing different characteristics of Chapala and to verify the accuracy of the model. We further demonstrate the usefulness of a 3D virtual reality environment and its potential importance in decision-making system development.
-
Multi-Scale Coupling Between Monte Carlo Molecular Simulation and Darcy-Scale Flow in Porous Media(Procedia Computer Science, Elsevier BV, 2016-06-02) [Conference Paper]In this work, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell centered finite difference method with non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational times by MC simulations from hours to seconds. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and the Darcy's one in reservoir simulators. This leads to an accurate description of thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.
-
PathlinesExplorer — Image-based exploration of large-scale pathline fields(2015 IEEE Scientific Visualization Conference (SciVis), Institute of Electrical and Electronics Engineers (IEEE), 2016-03-10) [Conference Paper]PathlinesExplorer is a novel image-based tool, which has been designed to visualize large scale pathline fields on a single computer [7]. PathlinesExplorer integrates explorable images (EI) technique [4] with order-independent transparency (OIT) method [2]. What makes this method different is that it allows users to handle large data on a single workstation. Although it is a view-dependent method, PathlinesExplorer combines both exploration and modification of visual aspects without re-accessing the original huge data. Our approach is based on constructing a per-pixel linked list data structure in which each pixel contains a list of pathline segments. With this view-dependent method, it is possible to filter, color-code, and explore large-scale flow data in real-time. In addition, optimization techniques such as early-ray termination and deferred shading are applied, which further improves the performance and scalability of our approach.
-
Multisource reverse-time migration and full-waveform inversion on a GPGPU(72nd EAGE Conference and Exhibition incorporating SPE EUROPEC 2010, EAGE Publications, 2015-12-22) [Conference Paper]
-
Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues(Journal of Comparative Neurology, Wiley, 2015-08-11) [Article]Advances for application of electron microscopy to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions (3D). From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here, we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room where we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of electron microscopy (EM) preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to observe a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. This article is protected by copyright. All rights reserved.
-
Generation of ultra-sound during tape peeling(Scientific Reports, Springer Nature, 2014-03-21) [Article]We investigate the generation of the screeching sound commonly heard during tape peeling using synchronised high-speed video and audio acquisition. We determine the peak frequencies in the audio spectrum and, in addition to a peak frequency at the upper end of the audible range (around 20 kHz), we find an unexpected strong sound with a high-frequency far above the audible range, typically around 50 kHz. Using the corresponding video data, the origins of the key frequencies are confirmed as being due to the substructure "fracture" bands, which we herein observe in both high-speed continuous peeling motions and in the slip phases for stick-slip peeling motions.
-
Cultural heritage omni-stereo panoramas for immersive cultural analytics - From the Nile to the Hijaz(2013 8th International Symposium on Image and Signal Processing and Analysis (ISPA), Institute of Electrical and Electronics Engineers (IEEE), 2013-09) [Conference Paper]The digital imaging acquisition and visualization techniques described here provides a hyper-realistic stereoscopic spherical capture of cultural heritage sites. An automated dual-camera system is used to capture sufficient stereo digital images to cover a sphere or cylinder. The resulting stereo images are projected undistorted in VR systems providing an immersive virtual environment in which researchers can collaboratively study the important textural details of an excavation or historical site. This imaging technique complements existing technologies such as LiDAR or SfM providing more detailed textural information that can be used in conjunction for analysis and visualization. The advantages of this digital imaging technique for cultural heritage can be seen in its non-invasive and rapid capture of heritage sites for documentation, analysis, and immersive visualization. The technique is applied to several significant heritage sites in Luxor, Egypt and Saudi Arabia.
-
Poster: Virtual reality interaction using mobile devices(2013 IEEE Symposium on 3D User Interfaces (3DUI), Institute of Electrical and Electronics Engineers (IEEE), 2013-03) [Conference Paper]In this work we aim to implement and evaluate alternative approaches for interacting with virtual environments on mobile devices for navigation, object selection and manipulation. Interaction with objects in virtual worlds using traditional input such as current state-of-the-art devices is often difficult and could diminish the immersion and sense of presence when it comes to 3D virtual environment tasks. We have developed new methods to perform different kinds of interactions using a mobile device (e.g. a smartphone) both as input device, performing selection and manipulation of objects, and as output device, utilizing the screen as an extra view (virtual camera or information display). Our hypothesis is that interaction via mobile devices facilitates simple tasks like the ones described within immersive virtual reality systems. We present here our initial implementation and result. © 2013 IEEE.
-
Poster: Observing change in crowded data sets in 3D space - Visualizing gene expression in human tissues(2013 IEEE Symposium on 3D User Interfaces (3DUI), Institute of Electrical and Electronics Engineers (IEEE), 2013-03) [Conference Paper]We have been confronted with a real-world problem of visualizing and observing change of gene expression between different human tissues. In this paper, we are presenting a universal representation space based on two-dimensional gel electrophoresis as opposed to force-directed layouts encountered most often in similar problems. We are discussing the methods we devised to make observing change more convenient in a 3D virtual reality environment. © 2013 IEEE.
-
Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal(Advanced Materials, Wiley, 2012-09-05) [Article]The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
-
KAUST Campus and Visualization Laboratory(Vimeo, 2012-06-19) [Presentation, Video]A visual and textual overview of King Abdullah University of Science and Technology (KAUST) campus in the Kingdom of Saudi Arabia and KAUST Visualization Laboratory (KVL).
-
Democratizing rendering for multiple viewers in surround VR systems(2012 IEEE Symposium on 3D User Interfaces (3DUI), Institute of Electrical and Electronics Engineers (IEEE), 2012-03) [Conference Paper]We present a new approach for how multiple users' views can be rendered in a surround virtual environment without using special multi-view hardware. It is based on the idea that different parts of the screen are often viewed by different users, so that they can be rendered from their own view point, or at least from a point closer to their view point than traditionally expected. The vast majority of 3D virtual reality systems are designed for one head-tracked user, and a number of passive viewers. Only the head tracked user gets to see the correct view of the scene, everybody else sees a distorted image. We reduce this problem by algorithmically democratizing the rendering view point among all tracked users. Researchers have proposed solutions for multiple tracked users, but most of them require major changes to the display hardware of the VR system, such as additional projectors or custom VR glasses. Our approach does not require additional hardware, except the ability to track each participating user. We propose three versions of our multi-viewer algorithm. Each of them balances image distortion and frame rate in different ways, making them more or less suitable for certain application scenarios. Our most sophisticated algorithm renders each pixel from its own, optimized camera perspective, which depends on all tracked users' head positions and orientations. © 2012 IEEE.
-
KAUST Supercomputing Laboratory(Vimeo, 2011-11-15) [Video]KAUST has partnered with IBM to establish a Supercomputing Research Center. KAUST is hosting the Shaheen supercomputer, named after the Arabian falcon famed for its swiftness of flight. This 16-rack IBM Blue Gene/P system is equipped with 4 gigabyte memory per node and capable of 222 teraflops, making KAUST campus the site of one of the world’s fastest supercomputers in an academic environment. KAUST is targeting petaflop capability within 3 years.
-
Auralization in 3 VR systems with system-specific spatialization using Asset Manager's panner abstraction layer(Vimeo, 2011-05-25) [Video]This is a short clip intended for use at the NIME 2011 convention in a presentation by Zachary Seldess. Toshiro Yamada demonstrates the Auralization in 3 VR systems with system-specific spatialization using Asset Manager's panner abstraction layer at KAUST Visualization Laboratory. The demonstration includes: 1) NexCave: 5 loudspeakers + 1 subwoofer using VBAP panning method 2) Cornea: 20 loudspeakers + 4 subwoofers using a custom 20-channel panning method 3) MPR: 8 loudspeakers + 4 subwoofers using a custom 8-channel panning method Sound system development by Zachary Seldess, KAUST and Toshiro Yamada, UCSD
