ScaleTraversal: Creating Multi-Scale Biomedical Animation with Limited Hardware Resources
Authors: 
Richen Liu, Hansheng Wang, Hailong Wang, Siru Chen, Chufan Lai, Ayush Kumar, Siming ChenAuthors Info & Claims
Richen Liu, Hansheng Wang, Hailong Wang, Siru Chen, Chufan Lai, Ayush Kumar, Siming ChenAuthors Info & ClaimsPages 2603 - 2612
Abstract
We design ScaleTraversal, an interactive tool for creating multi-scale 3D demonstration animations with limited resources for users who are unavailable to access high performance machines such as clusters or super computers. It is difficult to create 3D demonstration animations for multi-scale data. First, it is challenging to strike a balance between flexibility and user friendliness to design the user interface in customizing demonstration animations. Second, the multi-scale biomedical data is often characterized as large-size so that it is hard for users to handle it by a desktop PC. We design an interactive bi-functional user interface to create multi-scale biomedical demonstration animations intuitively. It fully utilizes the strengths of graphical interface's user friendliness and textual interface's flexibility, which enables users to customize demonstration animations from macro-scales to meso- and micro-scales. Furthermore, we design three scale-based memory management strategies to solve the issues presented in multi-scale data, including a streaming data processing strategy, a scale-based data prefetching strategy and a GPU acceleration strategy for rendering. Finally, we conduct both quantitative evaluation and qualitative evaluation to demonstrate the efficiency, expressiveness and usability of ScaleTraversal.
References
[1]
Asan Agibetov, Ricardo Manuel Millan Vaquero, Karl-Ingo Friese, Giuseppe Patane, Michela Spagnuolo, and Franz-Erich Wolter. 2014. Integrated Visualization and Analysis of a Multi-scale Biomedical Knowledge Space. In EuroVis Workshop on Visual Analytics, Vol. 1. 1--5.
[2]
James P. Ahrens, Jonathan Woodring, David E. DeMarle, John Patchett, and Mathew Maltrud. 2009. Interactive Remote Large-Scale Data Visualization via Prioritized Multi-Resolution Streaming. In Workshop on Ultrascale Visualization (Portland, Oregon) (UltraVis '09, Vol. 1), Michael E. Papka Kwan-Liu Ma (Ed.). ACM, New York, NY, USA, 1--10.
[3]
Ali K. Al-Awami, Johanna Beyer, Hendrik Strobelt, Narayanan Kasthuri, Jeff W. Lichtman, Hanspeter Pfister, and Markus Hadwiger. 2014. NeuroLines: A Subway Map Metaphor forVisualizing Nanoscale Neuronal Connectivity. IEEE Transactions on Visualization and Computer Graphics, Vol. 20, 12 (2014), 2369--2378.
[4]
Emil Axelsson, Jonathas Costa, Cláudio Silva, Carter Emmart, Alexander Bock, and Anders Ynnerman. 2017. Dynamic Scene Graph: Enabling Scaling, Positioning, and Navigation in the Universe. Computer Graphics Forum, Vol. 36, 3 (2017), 459--468.
[5]
Johanna Beyer, Ali Al-Awami, Narayanan Kasthuri, Jeff W. Lichtman, Hanspeter Pfister, and Markus Hadwiger. 2013. ConnectomeExplorer: Query-Guided Visual Analysis of Large Volumetric Neuroscience Data. IEEE Transactions on Visualization and Computer Graphics, Vol. 19, 12 (2013), 2868 --2877.
[6]
Shane Blackett, David Bullivant, David Nickerson, and Peter Hunter. 2005. Multi-Scale and Multi-Physics Visualization. In ACM SIGGRAPH 2005 Posters (Los Angeles, California) (SIGGRAPH '05, Vol. 1), Juan Buhler (Ed.). Association for Computing Machinery, New York, NY, USA, 136--es.
[7]
Saeed Boorboor, Shreeraj Jadhav, Mala Ananth, David Talmage, Lorna Role, and Arie Kaufman. 2018. Visualization of Neuronal Structures in Wide-Field Microscopy Brain Images. IEEE Transactions on Visualization and Computer Graphics, Vol. 25, 1 (2018), 1018--1028.
[8]
Michael Bostock and Jeffrey Heer. 2009. Protovis: A Graphical Toolkit for Visualization. IEEE Transactions on Visualization and Computer Graphics, Vol. 15, 6 (2009), 1121--1128.
[9]
Kevin J Brown, Arvind K Sujeeth, Hyouk Joong Lee, Tiark Rompf, Hassan Chafi, Martin Odersky, and Kunle Olukotun. 2011. A heterogeneous parallel framework for domain-specific languages. In International Conference on Parallel Architectures and Compilation Techniques, Lawrence Rauchwerger (Ed.), Vol. 1. IEEE, CPS, Galveston, Texas, USA, 89--100.
[10]
Hyungsuk Choi, Woohyuk Choi, Tran Minh Quan, David Hildebrand, Hanspeter Pfister, and Won-Ki Jeong. 2014. Vivaldi: A Domain-Specific Language for Volume Processing and Visualization on Distributed Heterogeneous Systems. IEEE Transactions on Visualization and Computer Graphics, Vol. 20, 12 (2014), 2407--2416.
[11]
Gregory Cipriano, George N. Phillips Jr., and Michael Gleicher. 2009. Multi-Scale Surface Descriptors. IEEE Transactions on Visualization and Computer Graphics, Vol. 15, 6 (2009), 1201--1208.
[12]
Steve Cook, Gareth Jones, Stuart Kent, and Alan Cameron Wills. 2007. Domain-specific development with visual studio DSL tools. Pearson Education.
[13]
Valerio Cosentino, Massimo Tisi, and Javier Luis Cánovas Izquierdo. 2015. A model-driven approach to generate external DSLs from object-oriented apis. In International Conference on Current Trends in Theory and Practice of Informatics, Giuseppe F. Italiano, Tiziana Margaria-Steffen, Jaroslav Pokorny, Jean-Jacques Quisquater, and Roger Wattenhofer (Eds.), Vol. 1. Springer, 423--435.
[14]
Romuald Deshayes. 2013. A Domain-Specific Modeling Approach for Gestural Interaction. In IEEE Symposium on Visual Languages and Human-Centric Computing, Stefan Sauer Caitlin Kelleher, Margaret Burnett (Ed.), Vol. 1. 181--182. https://doi.org/10.1109/VLHCC.2013.6645275
[15]
Zhifei Ding, Jiahao Han, Rongtao Qian, Liming Shen, Siru Chen, Lingxin Yu, Yu Zhu, and Richen Liu. 2023. eBoF: Interactive Temporal Correlation Analysis for Ensemble Data Based on Bag-of-Features. IEEE Transactions on Big Data, Vol. 9, 9 (2023), 1726--1737.
[16]
Min Gao, Lijun Wang, Jingle Jia, Yimin Chen, Richen Liu, Liming Shen, Xueyi Chen, and Mingjun Su. 2019. Interactive Geological Visualization Based on Quadratic-Surface Distance Query. Journal of Electronic Imaging, Vol. 28, 2 (2019), 021009.
[17]
Leopold Grinberg, Joseph A. Insley, Vitali Morozov, Michael E. Papka, George Em Karniadakis, Dmitry Fedosov, and Kalyan Kumaran. 2011. A New Computational Paradigm in Multiscale Simulations: Application to Brain Blood Flow. In International Conference for High Performance Computing, Networking, Storage and Analysis (SC), Scott Lathrop (Ed.), Vol. 1. IEEE, Seattle, WA, USA, 1--12.
[18]
Sarkis Halladjian, David Kouril, Haichao Miao, Eduard Groeller, Ivan Viola, and Tobias Isenberg. 2022. Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance. IEEE Transactions on Visualization and Computer Graphics, Vol. 28, 10 (2022), 3456--3470.
[19]
Sarkis Halladjian, Haichao Miao, David Kouil, M. Eduard Gröller, Ivan Viola, and Tobias Isenberg. 2020. Scale Trotter: Illustrative Visual Travels Across Negative Scales. IEEE Transactions on Visualization and Computer Graphics, Vol. 26, 1 (2020), 654--664.
[20]
Bogdan Hnat and Sandra C. Chapman. 1999. Visualization of multi-scale data sets in self-organized criticality sandpile model. In IEEE International Conference on Information Visualization (Cat. No. PR00210). 470--475.
[21]
Danny Holten and Jarke J. Van Wijk. 2009. Force-Directed Edge Bundling for Graph Visualization. Computer Graphics Forum, Vol. 28, 3 (2009), 983--990.
[22]
Wei-Hsien Hsu, Kwan-Liu Ma, and Carlos Correa. 2011. A Rendering Framework for Multiscale Views of 3D Models. ACM Transactions Graphics, Vol. 30, 6 (dec 2011), 1--10.
[23]
Paul Hudak. 1996. Building domain-specific embedded languages. Comput. Surveys, Vol. 28, 4es (1996), 196--es.
[24]
Paul Hudak and Mark P Jones. 1994. Haskell vs. Ada vs. C vs. awk vs.... an experiment in software prototyping productivity. Contract, Vol. 14, 92-C (1994), 0153.
[25]
Joseph A. Insley, Leopold Grinberg, Dmitry A. Fedosov, Vitali Morozov, Bruce Caswell, Michael E. Papka, and Geroge Em Karniadakis. 2011. Blood Flow: Multi-Scale Modeling and Visualization. In The 2011 Companion on High Performance Computing Networking, Storage and Analysis Companion (Seattle, Washington, USA) (SC '11 Companion, Vol. 1), Scott Lathrop (Ed.). Association for Computing Machinery, New York, NY, USA, 139--140.
[26]
Arne N Johanson and Wilhelm Hasselbring. 2014. Hierarchical combination of internal and external domain-specific languages for scientific computing. In European Conference on Software Architecture Workshops, Uwe Zdun (Ed.), Vol. 1. 1--8.
[27]
Karlis Kaugars. 1998. Integrated Multi Scale Text Retrieval Visualization. In CHI 98 Conference Summary on Human Factors in Computing Systems (Los Angeles, California, USA) (CHI '98, Vol. 1), Arnold Lund Clare-Marie Karat (Ed.). Association for Computing Machinery, New York, NY, USA, 307--308.
[28]
Gordon L. Kindlmann, Charisee Chiw, Nicholas Seltzer, Lamont Samuels, and John H. Reppy. 2016. Diderot: a Domain-Specific Language for Portable Parallel Scientific Visualization and Image Analysis. IEEE Transactions on Visualization and Computer Graphics, Vol. 22, 1 (2016), 867--876.
[29]
Tobias Klein, Ivan Viola, Eduard Gröller, and Peter Mindek. 2020. Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data. IEEE Transactions on Visualization and Computer Graphics, Vol. 26, 1 (2020), 622--632.
[30]
Robert Krueger, Johanna Beyer, Won-Dong Jang, Nam Wook Kim, Artem Sokolov, Peter K. Sorger, and Hanspeter Pfister. 2020. Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data. IEEE Transactions on Visualization and Computer Graphics, Vol. 26, 1 (2020), 227--237.
[31]
Mingzhao Li, Zhifeng Bao, Farhana Choudhury, and Timos Sellis. 2018. Supporting Large-Scale Geographical Visualization in a Multi-Granularity Way. In The Eleventh ACM International Conference on Web Search and Data Mining (Marina Del Rey, CA, USA) (WSDM '18, Vol. 1), Chengxiang Zhai Yi Chang (Ed.). Association for Computing Machinery, New York, NY, USA, 767--770.
[32]
Norbert Lindow, Daniel Baum, Morgan Leborgne, and Hans-Christian Hege. 2018. Interactive Visualization of RNA and DNA Structures. IEEE Transactions on Visualization and Computer Graphics, Vol. 25, 1 (2018), 967--976.
[33]
Richen Liu, Min Gao, Shunlong Ye, and Jiang Zhang. 2021. IGScript: An Interaction Grammar for Scientific Data Presentation. In ACM CHI Conference on Human Factors in Computing Systems (Yokohama, Japan) (CHI '21, Vol. 1). ACM, New York, NY, USA, Article 26, 13 pages.
[34]
Richen Liu, Hailong Wang, Chuyu Zhang, Xiaojian Chen, Lijun Wang, Genlin Ji, Bin Zhao, Zhiwei Mao, and Dan Yang. 2021. Narrative Scientific Data Visualization in an Immersive Environment. Bioinformatics, Vol. 37, 14 (2021), 2033--2041.
[35]
Richen Liu, Shunlong Ye, Zhifei Ding, Guang Yang, Shenghui Cheng, and Klaus Mueller. 2024. DRCmpVis: Visual Comparison of Physical Targets in Mobile Diminished and Mixed Reality. IEEE Transactions on Visualization and Computer Graphics, Vol. Early Access (2024), 1--14. https://doi.org/10.1109/TVCG.2024.3358419
[36]
Weifeng Ma, Qianggen Yang, Xiangdan Tang, and Shengshan Hou. 2010. A 3D visualization and management framework for geological disaster monitoring and early warning based on virtual globes. In The 18th International Conference on Geoinformatics, Aijun Chen Yu Liu (Ed.), Vol. 1. IEEE, Beijing, China, 1--5.
[37]
Ricardo Manuel Millan Vaquero, Asan Agibetov, Jan Rzepecki, Marta Ondresik, Alexander Vais, Joaquim Miguel Oliveira, Giuseppe Patane, Karl-Ingo Friese, Rui Luis Reis, Michela Spagnuolo, and Franz-Erich Wolter. 2015. A Semantically Adaptable Integrated Visualization and Natural Exploration of Multi-scale Biomedical Data. In The 19th International Conference on Information Visualisation, Vol. 1. IEEE, Barcelona, Spain, 543--552.
[38]
Robert Miller, Vadim Mozhayskiy, Llias Tagkopoulos, and Kwan-Liu Ma. 2011. EVEVis: A Multi-Scale Visualization System for Dense Evolutionary Data. In IEEE Symposium on Biological Data Visualization (BioVis), Vol. 1. IEEE, 143--150.
[39]
Haneen Mohammed, Ali K. Al-Awami, Johanna Beyer, Corrado Cali, Pierre Magistretti, Hanspeter Pfister, and Markus Hadwiger. 2018. Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells. IEEE Transactions on Visualization and Computer Graphics, Vol. 24, 1 (2018), 853--861.
[40]
Duong B. Nguyen, Rodolfo Ostilla Monico, and Guoning Chen. 2021. A Visualization Framework for Multi-scale Coherent Structures in Taylor-Couette Turbulence. IEEE Transactions on Visualization and Computer Graphics, Vol. 27, 2 (2021), 902--912.
[41]
Thammathip Piumsomboon, Gun A. Lee, Barrett Ens, Bruce H. Thomas, and Mark Billinghurst. 2018. Superman vs Giant: A Study on Spatial Perception for a Multi-Scale Mixed Reality Flying Telepresence Interface. IEEE Transactions on Visualization and Computer Graphics, Vol. 24, 11 (Nov 2018), 2974--2982.
[42]
Jonathan Ragan-Kelley, Andrew Adams, Sylvain Paris, Marc Levoy, Saman P. Amarasinghe, and Frédo Durand. 2012. Decoupling algorithms from schedules for easy optimization of image processing pipelines. ACM Transactions on Graphics, Vol. 31, 4 (2012), 32:1--32:12.
[43]
Peter Rautek, Stefan Bruckner, Eduard Gröller, and Markus Hadwiger. 2014. ViSlang: A System for Interpreted Domain-Specific Languages for Scientific Visualization. IEEE Transactions on Visualization and Computer Graphics, Vol. 20, 12 (2014), 2388--2396.
[44]
Jan Rzepecki, Ricardo Manuel Millán Vaquero, Alexander Vais, Karl-Ingo Friese, and Franz-Erich Wolter. 2014. Multimodal Approach for Natural Biomedical Multi-scale Exploration. In Advances in Visual Computing, Vol. 1. Springer, Las Vegas, NV, USA, 620--631.
[45]
Joris Sansen, Patricia Thébault, Isabelle Dutour, and Romain Bourqui. 2016. Visualization of sRNA-mRNA Interaction Predictions. In The 20th International Conference Information Visualisation (IV), Ebad Banissi, Mark W. McK. Bannatyne, Fatma Bouali, Remo Burkhard, John Counsell, Urska Cvek, Martin J. Eppler, Georges G. Grinstein, Weidong Huang, Sebastian Kernbach, Chun-Cheng Lin, Feng Lin, Francis T. Marchese, Chi Man Pun, Muhammad Sarfraz, Marjan Trutschl, Anna Ursyn, Gilles Venturini, Theodor G. Wyeld, and Jian J. Zhang (Eds.), Vol. 1. IEEE, Lisbon, Portugal, 342--347.
[46]
Max Schlee and Jean Vanderdonckt. 2004. Generative programming of graphical user interfaces. In The Working Conference on Advanced Visual Interfaces, Maria Francesca Costabile (Ed.), Vol. 1. 403--406.
[47]
Liming Shen, Xueyi Chen, Richen Liu, Hailong Wang, and GenLin Ji. 2021. Domain-Specific Language Techniques for Visual Computing: A Comprehensive Study. Archives of Computational Methods in Engineering, Vol. 28, 4 (2021), 3113--3134.
[48]
Yong Wan, Hideo Otsuna, Chi-Bin Chien, and Charles Hansen. 2009. An interactive visualization tool for multi-channel confocal microscopy data in neurobiology research. IEEE Transactions on Visualization and Computer Graphics, Vol. 15, 6 (2009), 1489--1496.
[49]
Chao Xu, Rui Wang, Shuang Zhao, and Hujun Bao. 2021. Multi-Scale Hybrid Micro-Appearance Modeling and Realtime Rendering of Thin Fabrics. IEEE Transactions on Visualization and Computer Graphics, Vol. 27, 4 (April 2021), 2409--2420.
[50]
Uwe Zdun and Mark Strembeck. 2009. Reusable architectural decisions for DSL design: Foundational decisions in DSLs development. In European Conference on Pattern Languages of Programs.
Index Terms
- ScaleTraversal: Creating Multi-Scale Biomedical Animation with Limited Hardware Resources
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October 2024
11719 pages
ISBN:9798400706868
DOI:10.1145/3664647
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Published: 28 October 2024
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