2018
Mika, Matthieu; Mion, Christophe
DEVICE FOR ANALYZING THE SYNCHRONIZATION OF IMAGES ON DIFFERENT DISPLAY PATHS Patent
2018.
Abstract | Links | BibTeX | Tags:
@patent{Mika2018b,
title = {DEVICE FOR ANALYZING THE SYNCHRONIZATION OF IMAGES ON DIFFERENT DISPLAY PATHS},
author = {Matthieu Mika and Christophe Mion},
url = {https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2018142049},
year = {2018},
date = {2018-08-09},
urldate = {2019-12-11},
abstract = {A device (DA) for analyzing a system (SI) comprising display means (PI1, EA1; PI2, EA2) responsible for displaying images, graphics cards (CG1, CG2) responsible for defining said images, and synchronization means (MS) for synchronizing the times of identical image definition by the graphics cards (CG1, CG2). This device (DA) comprises sensors (C1, C2) associated with display means (PI1, EA1; PI2, EA2) and generating a main signal representing a new image in case of detection of the display of one such new image by the associated display means, and analysis means (MA) responsible for determining a first time of reception of each of the main signals, then, when the first times of reception determined are representative of a same new image, determining a first time difference between said first times of reception determined.},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
A device (DA) for analyzing a system (SI) comprising display means (PI1, EA1; PI2, EA2) responsible for displaying images, graphics cards (CG1, CG2) responsible for defining said images, and synchronization means (MS) for synchronizing the times of identical image definition by the graphics cards (CG1, CG2). This device (DA) comprises sensors (C1, C2) associated with display means (PI1, EA1; PI2, EA2) and generating a main signal representing a new image in case of detection of the display of one such new image by the associated display means, and analysis means (MA) responsible for determining a first time of reception of each of the main signals, then, when the first times of reception determined are representative of a same new image, determining a first time difference between said first times of reception determined.
Mika, Matthieu; Mion, Christophe
2018.
Abstract | Links | BibTeX | Tags:
@patent{Mika2018,
title = {ANALYSIS DEVICE FOR DETERMINING A DETECTION TIME THAT CONTRIBUTES TO A LATENCY TIME WITHIN AN IMMERSIVE SYSTEM OF VIRTUAL REALITY},
author = {Matthieu Mika and Christophe Mion},
url = {https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2018142043},
year = {2018},
date = {2018-08-09},
urldate = {2018-08-09},
abstract = {The invention relates to a device (DA) performing analyses in an immersive virtual reality system, comprising a target (CD) secured to an object (O) that can move in a space (EP), and detection means (MD) for detecting the current position of said target (CD) in said space (EP) and delivering a first signal representing said current position. Said device (DA) comprises a sensor (CC) for generating a second signal when the object (O) reaches a known position in the space (EP), and analysis means (MA) that are coupled to the sensor (CC) and detection means (MD) and are used to determine a first time when a first signal representing said known detected position is received, and a second time when said second signal is received, and then to detemine a temporal distance between the determined first and second receiving times.},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
The invention relates to a device (DA) performing analyses in an immersive virtual reality system, comprising a target (CD) secured to an object (O) that can move in a space (EP), and detection means (MD) for detecting the current position of said target (CD) in said space (EP) and delivering a first signal representing said current position. Said device (DA) comprises a sensor (CC) for generating a second signal when the object (O) reaches a known position in the space (EP), and analysis means (MA) that are coupled to the sensor (CC) and detection means (MD) and are used to determine a first time when a first signal representing said known detected position is received, and a second time when said second signal is received, and then to detemine a temporal distance between the determined first and second receiving times.
2014
Vazquez-Duchêne, Marie-Danielle; Mion, Christophe; Mine, Solène; Jeanmaire, Christine; Freis, Olga; Pauly, Gilles; Hérault, David
Going into the Skin with Virtual Reality Book Chapter
In: Virtual Reality: Technologies, Medical Applications and Challenges, pp. 125–134, Nova Science Publishers, 2014.
Abstract | Links | BibTeX | Tags:
@inbook{Vazquez-Duchene2014,
title = {Going into the Skin with Virtual Reality},
author = {Marie-Danielle Vazquez-Duchêne and Christophe Mion and Solène Mine and Christine Jeanmaire and Olga Freis and Gilles Pauly and David Hérault},
url = {https://novapublishers.com/shop/virtual-reality-technologies-medical-applications-and-challenges/},
year = {2014},
date = {2014-12-01},
urldate = {2014-12-01},
booktitle = {Virtual Reality: Technologies, Medical Applications and Challenges},
pages = {125--134},
publisher = {Nova Science Publishers},
abstract = {The skin microanatomy is a complex structure that cannot be elucidated through traditional anatomical schema, description or illustration. To understand the human skin microanatomy and figure out relationships between cutaneous elements,a powerful tool has been setup since 2009. It is called the SkinExplorer™ platform and it offers to users to live a Virtual Reality (VR) experience. Once a series of images have been reconstructed into 3D cutaneous models, the platform allows manipulating them for scientific visualization and interpretation. The proposed VR system has mainly been developed to interact with tracked flystick and glasses. Furthermore, the goalis topropose a 3D immersive virtual reality experienceto move in depth into the skin. Living VR experience of the skin needs 3 main components: virtual environment, interface and the user. Benefits are numerous in terms of exploration: the selection of region of interest, interaction with large amplitude (zoom, translation and rotation) and applications of imaging treatments. The purpose is to provide to the user a range of access options to understand and explore the skin microanatomy. Even if the histological data is complex to obtain, the visual computing method remains intuitive, effective and accurate. This chapter will present the prototyped platform which is a promising innovative system to study human skin microanatomy and the related biological mechanisms.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
The skin microanatomy is a complex structure that cannot be elucidated through traditional anatomical schema, description or illustration. To understand the human skin microanatomy and figure out relationships between cutaneous elements,a powerful tool has been setup since 2009. It is called the SkinExplorer™ platform and it offers to users to live a Virtual Reality (VR) experience. Once a series of images have been reconstructed into 3D cutaneous models, the platform allows manipulating them for scientific visualization and interpretation. The proposed VR system has mainly been developed to interact with tracked flystick and glasses. Furthermore, the goalis topropose a 3D immersive virtual reality experienceto move in depth into the skin. Living VR experience of the skin needs 3 main components: virtual environment, interface and the user. Benefits are numerous in terms of exploration: the selection of region of interest, interaction with large amplitude (zoom, translation and rotation) and applications of imaging treatments. The purpose is to provide to the user a range of access options to understand and explore the skin microanatomy. Even if the histological data is complex to obtain, the visual computing method remains intuitive, effective and accurate. This chapter will present the prototyped platform which is a promising innovative system to study human skin microanatomy and the related biological mechanisms.
Vazquez-Duchêne, Marie-Danielle; Mion, Christophe; Mine, Solène; Jeanmaire, Christine; Freis, Olga; Pauly, Gilles; Courtois, Aurélie; Denis, Alain
VRIC '14: Proceedings of the 2014 Virtual Reality International Conference, Association for Computing Machinery, 2014.
Abstract | Links | BibTeX | Tags:
@conference{Marie-Danielle2014,
title = {Improving the human skin microanatomy understanding and skin aging observation with the SkinExplorer™ platform},
author = {Marie-Danielle Vazquez-Duchêne and Christophe Mion and Solène Mine and Christine Jeanmaire and Olga Freis and Gilles Pauly and Aurélie Courtois and Alain Denis},
doi = {10.1145/2617841.2620694},
year = {2014},
date = {2014-04-09},
urldate = {2014-04-09},
booktitle = {VRIC '14: Proceedings of the 2014 Virtual Reality International Conference},
pages = {1--4},
publisher = {Association for Computing Machinery},
abstract = {Background: The skin includes 3 major layers: epidermis, dermis and hypodermis. With aging, the human skin becomes thinner and flattens with dermal papillae being less pronounced. The epidermis becomes fine-drawn and the dermal network deteriorates with decades. The three-dimensional structure of elastic network and the hyaluronic acid distribution are so complex, rich and dense that the conventional observation ways can only provide partial view of these components.
Objective: The aim of this study was to demonstrate the morphological differences between two abdominal skin samples coming from young and aged donors based on elastic fibers organization and hyaluronic acid distribution.
Methods: The SkinExplorer™ platform performs immersive and interactive exploration with virtual reality applications.
Results: 2mm3 of histological data were obtained from 40 serial histological sections. Two three-dimensional numerical models from respectively young and aged skin biopsies were reconstructed. The observations were realized on the epidermis and dermal elastic fibers with the SkinExplorer™ platform and virtual reality (VR) applications. For hyaluronic acid repartition, two smaller models were reconstructed to see their richness and density by the same platform and VR tools.
Conclusion: These results suggest that Virtual Reality applications can be a good tool for the observation of aging process with its assessing and understanding. Moreover, this tool of exploration offers new way of micro-anatomical research.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Background: The skin includes 3 major layers: epidermis, dermis and hypodermis. With aging, the human skin becomes thinner and flattens with dermal papillae being less pronounced. The epidermis becomes fine-drawn and the dermal network deteriorates with decades. The three-dimensional structure of elastic network and the hyaluronic acid distribution are so complex, rich and dense that the conventional observation ways can only provide partial view of these components.
Objective: The aim of this study was to demonstrate the morphological differences between two abdominal skin samples coming from young and aged donors based on elastic fibers organization and hyaluronic acid distribution.
Methods: The SkinExplorer™ platform performs immersive and interactive exploration with virtual reality applications.
Results: 2mm3 of histological data were obtained from 40 serial histological sections. Two three-dimensional numerical models from respectively young and aged skin biopsies were reconstructed. The observations were realized on the epidermis and dermal elastic fibers with the SkinExplorer™ platform and virtual reality (VR) applications. For hyaluronic acid repartition, two smaller models were reconstructed to see their richness and density by the same platform and VR tools.
Conclusion: These results suggest that Virtual Reality applications can be a good tool for the observation of aging process with its assessing and understanding. Moreover, this tool of exploration offers new way of micro-anatomical research.
Objective: The aim of this study was to demonstrate the morphological differences between two abdominal skin samples coming from young and aged donors based on elastic fibers organization and hyaluronic acid distribution.
Methods: The SkinExplorer™ platform performs immersive and interactive exploration with virtual reality applications.
Results: 2mm3 of histological data were obtained from 40 serial histological sections. Two three-dimensional numerical models from respectively young and aged skin biopsies were reconstructed. The observations were realized on the epidermis and dermal elastic fibers with the SkinExplorer™ platform and virtual reality (VR) applications. For hyaluronic acid repartition, two smaller models were reconstructed to see their richness and density by the same platform and VR tools.
Conclusion: These results suggest that Virtual Reality applications can be a good tool for the observation of aging process with its assessing and understanding. Moreover, this tool of exploration offers new way of micro-anatomical research.
2013
Gonzalez, Alain; Sigoigne, Thomas; Mion, Christophe
2013.
Abstract | Links | BibTeX | Tags:
@patent{Gonzalez2013,
title = {Method for distributing rendering load of graphics processors to render evolutionary three-dimensional virtual scene of virtual world, involves allocating graphics processors to each view point according to comparison of computing times},
author = {Alain Gonzalez and Thomas Sigoigne and Christophe Mion},
editor = {e},
url = {https://patentscope.wipo.int/search/en/detail.jsf?docId=FR185968538},
year = {2013},
date = {2013-05-24},
urldate = {2016-02-26},
abstract = {The method involves calculating a rendering computing time for each of a series of view points (110) from allocation of a series of graphics processors determined during an iteration of the processors. Another rendering computing time of the iteration is estimated (120) for the view point by removing or adding the processors to the allocation of the processors determined during the iteration of the processors. The series of graphics processors is allocated (160) to the view point according to a comparison (130) of the estimated computing times. Independent claims are also included for the following: (1) a computing device comprising a processor linked to a programmable memory for implementing a method for distributing a rendering load of a series of graphics processors (2) a computer system (3) a computer medium comprising a program in memory for executing a method for distributing a rendering load of a series of graphics processors to render a series of view points of an evolutionary three-dimensional (3D) virtual scene.},
keywords = {},
pubstate = {published},
tppubtype = {patent}
}
The method involves calculating a rendering computing time for each of a series of view points (110) from allocation of a series of graphics processors determined during an iteration of the processors. Another rendering computing time of the iteration is estimated (120) for the view point by removing or adding the processors to the allocation of the processors determined during the iteration of the processors. The series of graphics processors is allocated (160) to the view point according to a comparison (130) of the estimated computing times. Independent claims are also included for the following: (1) a computing device comprising a processor linked to a programmable memory for implementing a method for distributing a rendering load of a series of graphics processors (2) a computer system (3) a computer medium comprising a program in memory for executing a method for distributing a rendering load of a series of graphics processors to render a series of view points of an evolutionary three-dimensional (3D) virtual scene.
Vazquez-Duchêne, Marie-Danielle; Mion, Christophe; Mine, Solène; Jeanmaire, Christine; Freis, Olga; Pauly, Gilles; Denis, Alain
Bringing Skin Observation to the Higher Level with 3D Immersive Virtual Environment Journal Article
In: International Journal of Computer Research, vol. 20, iss. 1, pp. 157–169, 2013.
Abstract | Links | BibTeX | Tags:
@article{Vazquez-Duchene2013b,
title = {Bringing Skin Observation to the Higher Level with 3D Immersive Virtual Environment},
author = {Marie-Danielle Vazquez-Duchêne and Christophe Mion and Solène Mine and Christine Jeanmaire and Olga Freis and Gilles Pauly and Alain Denis},
url = {https://novapublishers.com/shop/virtual-environments-developments-applications-and-challenges/},
year = {2013},
date = {2013-04-01},
urldate = {2013-04-01},
booktitle = {Virtual Environments: Developments, Applications and Challenges},
journal = {International Journal of Computer Research},
volume = {20},
issue = {1},
pages = {157--169},
publisher = {Nova Science Publishers},
series = {Computer Science, Technology and Applications},
abstract = {Sectioning biopsies for confocal microscopy observation poses various difficulties to the user in the 3D volumetric reconstruction model such as distortions and warping during the cutting with cryostat and the labeling of sections with antibodies. It results in a misalignment between sections which corresponds to the major challenge that needs to be solved with accuracy and efficiency.
Computer-based visualization of large volume has led to the creation of 3D virtual skin models near to microscopic reality. To be at micrometer level and use a microscope system for observing histological sections automatically reduces the field of view.
Virtual environment (VE) enhances the user capacities and gives to him a skin interpretation. Most of the time, VE is developed for training tasks but, in cosmetic research the immersive SkinExplorer(TM) platform has been set up for observing 3D reconstructed data.
The aim of the platform is to give to the user the ability to reconstruct the 3D model intuitively, effectively and accurately and finally to explore the architectural organization of the 3D model components. The skin observation by virtual environment provides appropriate insights, allows exploration and understanding of the spatial arrangement and structural characteristics of complex serial histological sections.
The overall goal is to propose a novel approach for construction, display, manipulation, interaction and scientific visualization of skin components with volumetric data from confocal microscopy acquisitions.
The innovative immersive platform already permits researchers to visualize cutaneous structural changes in elastic fibers network during chronological aging and premature photo aging or after stretch marks formation. Some investigations also show the effect of cosmetic treatment. In this chapter, the SkinExplorerTM platform proposes to "enter" into the spatial organization of specific cells such as melanocytes responsible for skin pigmentation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sectioning biopsies for confocal microscopy observation poses various difficulties to the user in the 3D volumetric reconstruction model such as distortions and warping during the cutting with cryostat and the labeling of sections with antibodies. It results in a misalignment between sections which corresponds to the major challenge that needs to be solved with accuracy and efficiency.
Computer-based visualization of large volume has led to the creation of 3D virtual skin models near to microscopic reality. To be at micrometer level and use a microscope system for observing histological sections automatically reduces the field of view.
Virtual environment (VE) enhances the user capacities and gives to him a skin interpretation. Most of the time, VE is developed for training tasks but, in cosmetic research the immersive SkinExplorer(TM) platform has been set up for observing 3D reconstructed data.
The aim of the platform is to give to the user the ability to reconstruct the 3D model intuitively, effectively and accurately and finally to explore the architectural organization of the 3D model components. The skin observation by virtual environment provides appropriate insights, allows exploration and understanding of the spatial arrangement and structural characteristics of complex serial histological sections.
The overall goal is to propose a novel approach for construction, display, manipulation, interaction and scientific visualization of skin components with volumetric data from confocal microscopy acquisitions.
The innovative immersive platform already permits researchers to visualize cutaneous structural changes in elastic fibers network during chronological aging and premature photo aging or after stretch marks formation. Some investigations also show the effect of cosmetic treatment. In this chapter, the SkinExplorerTM platform proposes to "enter" into the spatial organization of specific cells such as melanocytes responsible for skin pigmentation.
Computer-based visualization of large volume has led to the creation of 3D virtual skin models near to microscopic reality. To be at micrometer level and use a microscope system for observing histological sections automatically reduces the field of view.
Virtual environment (VE) enhances the user capacities and gives to him a skin interpretation. Most of the time, VE is developed for training tasks but, in cosmetic research the immersive SkinExplorer(TM) platform has been set up for observing 3D reconstructed data.
The aim of the platform is to give to the user the ability to reconstruct the 3D model intuitively, effectively and accurately and finally to explore the architectural organization of the 3D model components. The skin observation by virtual environment provides appropriate insights, allows exploration and understanding of the spatial arrangement and structural characteristics of complex serial histological sections.
The overall goal is to propose a novel approach for construction, display, manipulation, interaction and scientific visualization of skin components with volumetric data from confocal microscopy acquisitions.
The innovative immersive platform already permits researchers to visualize cutaneous structural changes in elastic fibers network during chronological aging and premature photo aging or after stretch marks formation. Some investigations also show the effect of cosmetic treatment. In this chapter, the SkinExplorerTM platform proposes to "enter" into the spatial organization of specific cells such as melanocytes responsible for skin pigmentation.
Vazquez-Duchêne, Marie-Danielle; Freis, Olga; Denis, Alain; Mion, Christophe; Jeanmaire, Christine; Mine, Solène; Pauly, Gilles
Virtual reality for skin exploration Conference
VRIC '13: Proceedings of the Virtual Reality International Conference: Laval Virtual, ACM, 2013.
Abstract | Links | BibTeX | Tags:
@conference{Vazquez-Duchene2013,
title = {Virtual reality for skin exploration},
author = {Marie-Danielle Vazquez-Duchêne and Olga Freis and Alain Denis and Christophe Mion and Christine Jeanmaire and Solène Mine and Gilles Pauly},
doi = {10.1145/2466816.2466822},
year = {2013},
date = {2013-03-20},
urldate = {2013-03-20},
booktitle = {VRIC '13: Proceedings of the Virtual Reality International Conference: Laval Virtual},
pages = {1--4},
publisher = {ACM},
abstract = {Background: We have developed and set up the SkinExplorer™ platform, a new tool to exploit and rebuild serial confocal images into 3D numerical models [1, 2]. The acquisitions using confocal microscopy allow visualizing cutaneous components as elastic fibers, melanocytes and keratinocytes etc... These diversified sources of data participate to create numerical 3D volume models with high quality of visualization.
Objective: To create a Virtual Reality (VR) experience, to communicate and change the perception of skin structures by virtualization mode.
Methods: The use of ART TRACKPACK system and ART SMARTTRACK device allow us to valorize new sensory images for the volumetric rendering of the 3D skin models.
Results: We increase the perception and the understanding of skin components organization.
Conclusion: The SkinExplorer™ platform seems to be a promising system for exploring the skin.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Background: We have developed and set up the SkinExplorer™ platform, a new tool to exploit and rebuild serial confocal images into 3D numerical models [1, 2]. The acquisitions using confocal microscopy allow visualizing cutaneous components as elastic fibers, melanocytes and keratinocytes etc... These diversified sources of data participate to create numerical 3D volume models with high quality of visualization.
Objective: To create a Virtual Reality (VR) experience, to communicate and change the perception of skin structures by virtualization mode.
Methods: The use of ART TRACKPACK system and ART SMARTTRACK device allow us to valorize new sensory images for the volumetric rendering of the 3D skin models.
Results: We increase the perception and the understanding of skin components organization.
Conclusion: The SkinExplorer™ platform seems to be a promising system for exploring the skin.
Objective: To create a Virtual Reality (VR) experience, to communicate and change the perception of skin structures by virtualization mode.
Methods: The use of ART TRACKPACK system and ART SMARTTRACK device allow us to valorize new sensory images for the volumetric rendering of the 3D skin models.
Results: We increase the perception and the understanding of skin components organization.
Conclusion: The SkinExplorer™ platform seems to be a promising system for exploring the skin.
Hoang, Thai V.; Cavin, Xavier; Schultz, Patrick; Ritchie, David
GEMpicker: A highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy Journal Article
In: BMC structural biology, vol. 13, pp. 25, 2013.
Abstract | Links | BibTeX | Tags:
@article{articleb,
title = {GEMpicker: A highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy},
author = {Thai V. Hoang and Xavier Cavin and Patrick Schultz and David Ritchie},
doi = {10.1186/1472-6807-13-25},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {BMC structural biology},
volume = {13},
pages = {25},
abstract = {Background
Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs.
Results
We have developed “gEMpicker”, a highly parallel correlation-based particle picking tool. To our knowledge, gEMpicker is the first particle picking program to use multiple graphics processor units (GPUs) to accelerate the calculation. When tested on the publicly available keyhole limpet hemocyanin dataset, we find that gEMpicker gives similar results to the FindEM program. However, compared to calculating correlations on one core of a contemporary central processor unit (CPU), running gEMpicker on a modern GPU gives a speed-up of about 27 ×. To achieve even higher processing speeds, the basic correlation calculations are accelerated considerably by using a hierarchy of parallel programming techniques to distribute the calculation over multiple GPUs and CPU cores attached to multiple nodes of a computer cluster. By using a theoretically optimal reduction algorithm to collect and combine the cluster calculation results, the speed of the overall calculation scales almost linearly with the number of cluster nodes available.
Conclusions
The very high picking throughput that is now possible using GPU-powered workstations or computer clusters will help experimentalists to achieve higher resolution 3D reconstructions more rapidly than before.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background
Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs.
Results
We have developed “gEMpicker”, a highly parallel correlation-based particle picking tool. To our knowledge, gEMpicker is the first particle picking program to use multiple graphics processor units (GPUs) to accelerate the calculation. When tested on the publicly available keyhole limpet hemocyanin dataset, we find that gEMpicker gives similar results to the FindEM program. However, compared to calculating correlations on one core of a contemporary central processor unit (CPU), running gEMpicker on a modern GPU gives a speed-up of about 27 ×. To achieve even higher processing speeds, the basic correlation calculations are accelerated considerably by using a hierarchy of parallel programming techniques to distribute the calculation over multiple GPUs and CPU cores attached to multiple nodes of a computer cluster. By using a theoretically optimal reduction algorithm to collect and combine the cluster calculation results, the speed of the overall calculation scales almost linearly with the number of cluster nodes available.
Conclusions
The very high picking throughput that is now possible using GPU-powered workstations or computer clusters will help experimentalists to achieve higher resolution 3D reconstructions more rapidly than before.
Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is the accurate and automatic picking of particles from raw cryo-electron micrographs.
Results
We have developed “gEMpicker”, a highly parallel correlation-based particle picking tool. To our knowledge, gEMpicker is the first particle picking program to use multiple graphics processor units (GPUs) to accelerate the calculation. When tested on the publicly available keyhole limpet hemocyanin dataset, we find that gEMpicker gives similar results to the FindEM program. However, compared to calculating correlations on one core of a contemporary central processor unit (CPU), running gEMpicker on a modern GPU gives a speed-up of about 27 ×. To achieve even higher processing speeds, the basic correlation calculations are accelerated considerably by using a hierarchy of parallel programming techniques to distribute the calculation over multiple GPUs and CPU cores attached to multiple nodes of a computer cluster. By using a theoretically optimal reduction algorithm to collect and combine the cluster calculation results, the speed of the overall calculation scales almost linearly with the number of cluster nodes available.
Conclusions
The very high picking throughput that is now possible using GPU-powered workstations or computer clusters will help experimentalists to achieve higher resolution 3D reconstructions more rapidly than before.
Hoang, Thai V.; Cavin, Xavier; Ritchie, David
GEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration Journal Article
In: Journal of structural biology, 2013.
Abstract | Links | BibTeX | Tags:
@article{articlec,
title = {GEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration},
author = {Thai V. Hoang and Xavier Cavin and David Ritchie},
doi = {10.1016/j.jsb.2013.09.010},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {Journal of structural biology},
abstract = {Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program.
2012
Cavin, Xavier; Demengeon, Olivier
Shift-Based Parallel Image Compositing on InfiniBandTM Fat-Trees Proceedings Article
In: 12th Eurographics Symposium on Parallel Graphics and Visualization, EGPGV@Eurographics 2012, Cagliari, Sardinia, Italy, May 13-14, 2012, pp. 129–138, Eurographics Association, 2012.
Abstract | Links | BibTeX | Tags:
@inproceedings{DBLP:conf/egpgv/CavinD12,
title = {Shift-Based Parallel Image Compositing on InfiniBandTM Fat-Trees},
author = {Xavier Cavin and Olivier Demengeon},
doi = {10.2312/EGPGV/EGPGV12/129-138},
year = {2012},
date = {2012-01-01},
urldate = {2012-01-01},
booktitle = {12th Eurographics Symposium on Parallel Graphics and Visualization, EGPGV@Eurographics 2012, Cagliari, Sardinia, Italy, May 13-14, 2012},
pages = {129–138},
publisher = {Eurographics Association},
abstract = {Parallel image compositing has been widely studied over the past 20 years, as this is one, if not the most, crucial element in the implementation of a scalable parallel rendering system. Many algorithms have been proposed and implemented on a large variety of supercomputers. Among the existing supercomputers, InfiniBandTM (IB) PC clusters, and their associated fat-tree topology, are clearly becoming the dominant architecture, as they provide the scalability, high bandwidth and low latency required by the most demanding parallel applications. Surprisingly, very few efforts have been devoted to the implementation and performance evaluation of parallel image compositing algorithms on this kind of architecture. We propose in this paper a new parallel image compositing algorithm, called Shift-Based, relying on a well-known communication pattern called shift permutation. Indeed, shift permutation is one of the possible ways to get the maximum cross bisectional bandwidth provided by an IB fat-tree cluster. We show that our Shift-Based algorithm scales on any number of processing nodes (with peak performance on specific counts), allows overlapping communications with computations and exhibits contentionfree network communications. This is demonstrated with the image compositing of very high resolution images at interactive frame rates.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Parallel image compositing has been widely studied over the past 20 years, as this is one, if not the most, crucial element in the implementation of a scalable parallel rendering system. Many algorithms have been proposed and implemented on a large variety of supercomputers. Among the existing supercomputers, InfiniBandTM (IB) PC clusters, and their associated fat-tree topology, are clearly becoming the dominant architecture, as they provide the scalability, high bandwidth and low latency required by the most demanding parallel applications. Surprisingly, very few efforts have been devoted to the implementation and performance evaluation of parallel image compositing algorithms on this kind of architecture. We propose in this paper a new parallel image compositing algorithm, called Shift-Based, relying on a well-known communication pattern called shift permutation. Indeed, shift permutation is one of the possible ways to get the maximum cross bisectional bandwidth provided by an IB fat-tree cluster. We show that our Shift-Based algorithm scales on any number of processing nodes (with peak performance on specific counts), allows overlapping communications with computations and exhibits contentionfree network communications. This is demonstrated with the image compositing of very high resolution images at interactive frame rates.
2006
Cavin, Xavier; Mion, Christophe
Pipelined Sort-last Rendering: Scalability, Performance and Beyond Proceedings Article
In: 6th Eurographics Symposium on Parallel Graphics and Visualization - EGPGV 2006, Braga, Portugal, 2006.
Abstract | Links | BibTeX | Tags:
@inproceedings{cavin:inria-00104990,
title = {Pipelined Sort-last Rendering: Scalability, Performance and Beyond},
author = {Xavier Cavin and Christophe Mion},
url = {https://inria.hal.science/inria-00104990},
year = {2006},
date = {2006-05-01},
urldate = {2006-05-01},
booktitle = {6th Eurographics Symposium on Parallel Graphics and Visualization - EGPGV 2006},
address = {Braga, Portugal},
abstract = {We present in this paper a theoretical and practical performance analysis of pipelined sort-last rendering for both polygonal and volume rendering. Theoretical peak performance and scalability are studied, exhibiting maximum attainable framerates of 19 fps (volume rendering with back-to-front alpha blending) and 11 fps (polygonal rendering with Z-buffer compositing) for a 1280×1024 display on a Gigabit Ethernet cluster. We show that our implementation of pipelined sort-last rendering on a 17-node PC cluster can nearly sustain these theoretical figures. We finally propose possible enhancements that would allow to go beyond the maximum theoretical limits. This paper clearly shows the potential of pipelined sort-last rendering for real-time visualization of very large models on standard PC clusters.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
We present in this paper a theoretical and practical performance analysis of pipelined sort-last rendering for both polygonal and volume rendering. Theoretical peak performance and scalability are studied, exhibiting maximum attainable framerates of 19 fps (volume rendering with back-to-front alpha blending) and 11 fps (polygonal rendering with Z-buffer compositing) for a 1280×1024 display on a Gigabit Ethernet cluster. We show that our implementation of pipelined sort-last rendering on a 17-node PC cluster can nearly sustain these theoretical figures. We finally propose possible enhancements that would allow to go beyond the maximum theoretical limits. This paper clearly shows the potential of pipelined sort-last rendering for real-time visualization of very large models on standard PC clusters.
Castanie, Laurent; Mion, Christophe; Cavin, Xavier; Lévy, Bruno
Distributed Shared Memory for Roaming Large Volumes Journal Article
In: IEEE Trans. Vis. Comput. Graph., vol. 12, no. 5, pp. 1299–1306, 2006.
Abstract | Links | BibTeX | Tags:
@article{DBLP:journals/tvcg/CastanieMCL06,
title = {Distributed Shared Memory for Roaming Large Volumes},
author = {Laurent Castanie and Christophe Mion and Xavier Cavin and Bruno Lévy},
doi = {10.1109/TVCG.2006.135},
year = {2006},
date = {2006-01-01},
urldate = {2006-01-01},
journal = {IEEE Trans. Vis. Comput. Graph.},
volume = {12},
number = {5},
pages = {1299–1306},
abstract = {We present a cluster-based volume rendering system for roaming very large volumes. This system allows to move a gigabyte-sized probe inside a total volume of several tens or hundreds of gigabytes in real-time. While the size of the probe is limited by the total amount of texture memory on the cluster, the size of the total data set has no theoretical limit. The cluster is used as a distributed graphics processing unit that both aggregates graphics power and graphics memory. A hardware-accelerated volume renderer runs in parallel on the cluster nodes and the final image compositing is implemented using a pipelined sort-last rendering algorithm. Meanwhile, volume bricking and volume paging allow efficient data caching. On each rendering node, a distributed hierarchical cache system implements a global software-based distributed shared memory on the cluster. In case of a cache miss, this system first checks page residency on the other cluster nodes instead of directly accessing local disks. Using two gigabit Ethernet network interfaces per node, we accelerate data fetching by a factor of 4 compared to directly accessing local disks. The system also implements asynchronous disk access and texture loading, which makes it possible to overlap data loading, volume slicing and rendering for optimal volume roaming},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a cluster-based volume rendering system for roaming very large volumes. This system allows to move a gigabyte-sized probe inside a total volume of several tens or hundreds of gigabytes in real-time. While the size of the probe is limited by the total amount of texture memory on the cluster, the size of the total data set has no theoretical limit. The cluster is used as a distributed graphics processing unit that both aggregates graphics power and graphics memory. A hardware-accelerated volume renderer runs in parallel on the cluster nodes and the final image compositing is implemented using a pipelined sort-last rendering algorithm. Meanwhile, volume bricking and volume paging allow efficient data caching. On each rendering node, a distributed hierarchical cache system implements a global software-based distributed shared memory on the cluster. In case of a cache miss, this system first checks page residency on the other cluster nodes instead of directly accessing local disks. Using two gigabit Ethernet network interfaces per node, we accelerate data fetching by a factor of 4 compared to directly accessing local disks. The system also implements asynchronous disk access and texture loading, which makes it possible to overlap data loading, volume slicing and rendering for optimal volume roaming
Zara, Florence; Haefele, Matthieu; Mion, Christophe; Dischler, Jean-Michel
Hypervolumetric Plasma-data Visualization Technical Report
INRIA no. RR-5971, 2006.
Abstract | Links | BibTeX | Tags:
@techreport{zara:inria-00090630,
title = {Hypervolumetric Plasma-data Visualization},
author = {Florence Zara and Matthieu Haefele and Christophe Mion and Jean-Michel Dischler},
url = {https://inria.hal.science/inria-00090630},
year = {2006},
date = {2006-01-01},
urldate = {2006-01-01},
number = {RR-5971},
pages = {16},
institution = {INRIA},
abstract = {Several techniques have been proposed to explore hypervolumetric datasets but most of them fail to be efficient when very large fields are to be processed. This report describes an interactive visualization technique designed to explore at real-time framerates very large hypervolumetric 4-D+t scalarfields (with up to 16GB raw data per time step). We introduce a new out-of-core scheme aiming at generalizing to hypervolumes, brick-based techniques, already standartly used for large volumetric (e. g. 3D) datasets. For a given time step, we visualize the entire 4-D space by displaying directly 2-D arrays of height fields, each height field representing a 2-D hyperslice of the 4-D space. The contribution of this work consists in introducing an efficient partitionning scheme, that we called hyper-bricks, in such a way that it overcomes all hardware bottlenecks, namely the progressive load from disk, the decompression time (CPU) and the display time (GPU). We show that our technique, further using a cache system and a level of detail representation allows users to explore the full hypervolume at real-time framerates even on low-end PCs with basic graphics cards. We mainly apply our technique to the interactive exploration of plasma behaviors resulting from large numerical semi-Lagrangian simulations.
},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
Several techniques have been proposed to explore hypervolumetric datasets but most of them fail to be efficient when very large fields are to be processed. This report describes an interactive visualization technique designed to explore at real-time framerates very large hypervolumetric 4-D+t scalarfields (with up to 16GB raw data per time step). We introduce a new out-of-core scheme aiming at generalizing to hypervolumes, brick-based techniques, already standartly used for large volumetric (e. g. 3D) datasets. For a given time step, we visualize the entire 4-D space by displaying directly 2-D arrays of height fields, each height field representing a 2-D hyperslice of the 4-D space. The contribution of this work consists in introducing an efficient partitionning scheme, that we called hyper-bricks, in such a way that it overcomes all hardware bottlenecks, namely the progressive load from disk, the decompression time (CPU) and the display time (GPU). We show that our technique, further using a cache system and a level of detail representation allows users to explore the full hypervolume at real-time framerates even on low-end PCs with basic graphics cards. We mainly apply our technique to the interactive exploration of plasma behaviors resulting from large numerical semi-Lagrangian simulations.
2005
Luo, Shi-Whei; Ray, Nicolas; Cavin, Xavier; Maigret, Bernard
Statistical analysis of protein-protein interactions: Organization and contribution of interfacial residues Proceedings Article
In: Journées Ouvertes Biologie Informatique Mathématiques JOBIM 2005, Lyon, France, 2005.
@inproceedings{luo:inria-00000445,
title = {Statistical analysis of protein-protein interactions: Organization and contribution of interfacial residues},
author = {Shi-Whei Luo and Nicolas Ray and Xavier Cavin and Bernard Maigret},
url = {https://inria.hal.science/inria-00000445},
year = {2005},
date = {2005-07-01},
booktitle = {Journées Ouvertes Biologie Informatique Mathématiques JOBIM 2005},
address = {Lyon, France},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Ray, Nicolas; Cavin, Xavier; Levy, Bruno
Vector Texture Mapping on the GPU Proceedings Article
In: 25th gOcad Meeting, ASGA, 2005.
@inproceedings{RayRM2005a,
title = {Vector Texture Mapping on the GPU},
author = {Nicolas Ray and Xavier Cavin and Bruno Levy},
year = {2005},
date = {2005-06-01},
booktitle = {25th gOcad Meeting},
publisher = {ASGA},
abstract = {This paper presents VTMs (Vector Texture Maps), a novel representation of vector images that can be used as a texture by the GPU for real-time rendering. A VTM decomposes texture space into different regions, represented in an analytic way, by a set of implicit degree 3 polynomials. Each region can be rendered by a different fragment shading function. Accurate anti-aliasing is performed in real-time, based on an estimate of fragment coverage. As a consequence, infinite zooming can be applied without any pixel discretization artifact. Based on a hierarchical data structure, our representation has low memory requirements. Its versatility is demonstrated in various settings, including a font engine completely implemented in the GPU.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
This paper presents VTMs (Vector Texture Maps), a novel representation of vector images that can be used as a texture by the GPU for real-time rendering. A VTM decomposes texture space into different regions, represented in an analytic way, by a set of implicit degree 3 polynomials. Each region can be rendered by a different fragment shading function. Accurate anti-aliasing is performed in real-time, based on an estimate of fragment coverage. As a consequence, infinite zooming can be applied without any pixel discretization artifact. Based on a hierarchical data structure, our representation has low memory requirements. Its versatility is demonstrated in various settings, including a font engine completely implemented in the GPU.
Cavin, Xavier; Mion, Christophe; Filbois, Alain
COTS Cluster-based Sort-last Rendering: Performance Evaluation and Pipelined Implementation Proceedings Article
In: 16th IEEE Visualization Conference, IEEE Vis 2005, Minneapolis, MN, USA, October 23-28, 2005, Proceedings, pp. 111–118, IEEE Computer Society, 2005.
@inproceedings{DBLP:conf/visualization/CavinMF05,
title = {COTS Cluster-based Sort-last Rendering: Performance Evaluation and
Pipelined Implementation},
author = {Xavier Cavin and Christophe Mion and Alain Filbois},
url = {https://doi.org/10.1109/VISUAL.2005.1532785},
doi = {10.1109/VISUAL.2005.1532785},
year = {2005},
date = {2005-01-01},
booktitle = {16th IEEE Visualization Conference, IEEE Vis 2005, Minneapolis,
MN, USA, October 23-28, 2005, Proceedings},
pages = {111–118},
publisher = {IEEE Computer Society},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Ray, Nicolas; Cavin, Xavier; Paul, Jean-Claude; Maigret, Bernard
Intersurf: dynamic interface between proteins Journal Article
In: Journal of Molecular Graphics and Modelling, vol. 23, no. 4, pp. 347-354, 2005.
@article{ray:inria-00105634,
title = {Intersurf: dynamic interface between proteins},
author = {Nicolas Ray and Xavier Cavin and Jean-Claude Paul and Bernard Maigret},
url = {https://inria.hal.science/inria-00105634},
doi = {10.1016/j.jmgm.2004.11.004},
year = {2005},
date = {2005-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {23},
number = {4},
pages = {347-354},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2004
Mion, Christophe; Zara, Florence; Dischler, Jean-Michel
Interactive out-of-core visualisation of 4-D+t plasma data Technical Report
INRIA no. RR-5444, 2004.
@techreport{mion:inria-00070563,
title = {Interactive out-of-core visualisation of 4-D+t plasma data},
author = {Christophe Mion and Florence Zara and Jean-Michel Dischler},
url = {https://inria.hal.science/inria-00070563},
year = {2004},
date = {2004-01-01},
number = {RR-5444},
pages = {28},
institution = {INRIA},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
2003
Gribble, Christiaan; Cavin, Xavier; Hartner, Mark; Hansen, Charles
Cluster-Based Interactive Volume Rendering with Simian Technical Report
School of Computing University of Utah no. UUCS-03-017, 2003.
Abstract | Links | BibTeX | Tags:
@techreport{Gribble2003,
title = {Cluster-Based Interactive Volume Rendering with Simian},
author = {Christiaan Gribble and Xavier Cavin and Mark Hartner and Charles Hansen},
url = {https://users.cs.utah.edu/docs/techreports/2003/pdf/UUCS-03-017.pdf},
year = {2003},
date = {2003-09-03},
number = {UUCS-03-017},
institution = {School of Computing University of Utah},
abstract = {Commodity-based computer clusters offer a cost-effective alternative to traditional large scale, tightly coupled computers as a means to provide high-performance computational and visualization services. The Center for the Simulation of Accidental Fires and Explosions (C-SAFE) at the University of Utah employs such a cluster, and we have begun to experiment with cluster-based visualization services. In particular, we seek to develop an interactive volume rendering tool for navigating and visualizing large-scale scientific datasets. Using Simian, an OpenGL volume renderer, we examine two approaches to cluster-based interactive volume rendering: (1) a “cluster-aware” version of the application that makes explicit use of remote nodes through a message-passing interface, and (2) the unmodified application running atop the Chromium clustered rendering framework. This paper provides a detailed comparison of the two approaches by carefully considering the key issues that arise when parallelizing Simian. These issues include the richness of user interaction; the distribution of volumetric datasets and proxy geometry; and the degree of interactivity provided by the image rendering and compositing schemes. The results of each approach when visualizing two large-scale C-SAFE datasets are given, and we discuss the relative advantages and disadvantages that were considered when developing our cluster-based interactive volume rendering application.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
Commodity-based computer clusters offer a cost-effective alternative to traditional large scale, tightly coupled computers as a means to provide high-performance computational and visualization services. The Center for the Simulation of Accidental Fires and Explosions (C-SAFE) at the University of Utah employs such a cluster, and we have begun to experiment with cluster-based visualization services. In particular, we seek to develop an interactive volume rendering tool for navigating and visualizing large-scale scientific datasets. Using Simian, an OpenGL volume renderer, we examine two approaches to cluster-based interactive volume rendering: (1) a “cluster-aware” version of the application that makes explicit use of remote nodes through a message-passing interface, and (2) the unmodified application running atop the Chromium clustered rendering framework. This paper provides a detailed comparison of the two approaches by carefully considering the key issues that arise when parallelizing Simian. These issues include the richness of user interaction; the distribution of volumetric datasets and proxy geometry; and the degree of interactivity provided by the image rendering and compositing schemes. The results of each approach when visualizing two large-scale C-SAFE datasets are given, and we discuss the relative advantages and disadvantages that were considered when developing our cluster-based interactive volume rendering application.
Ray, Nicolas; Ulysse, Jean-Christophe; Cavin, Xavier; Lévy, Bruno
Generation of Radiosity Texture Atlas for Realistic Real-Time Rendering Proceedings Article
In: Chover, Miguel; Hagen, Hans; Tost, Daniela (Ed.): 24th Annual Conference of the European Association for Computer Graphics, Eurographics 2003 - Short Presentations, Granada, Spain, September 1-5, 2003, Eurographics Association, 2003.
@inproceedings{DBLP:conf/eurographics/RayUCL03,
title = {Generation of Radiosity Texture Atlas for Realistic Real-Time Rendering},
author = {Nicolas Ray and Jean-Christophe Ulysse and Xavier Cavin and Bruno Lévy},
editor = {Miguel Chover and Hans Hagen and Daniela Tost},
url = {https://doi.org/10.2312/egs.20031064},
doi = {10.2312/EGS.20031064},
year = {2003},
date = {2003-01-01},
booktitle = {24th Annual Conference of the European Association for Computer Graphics,
Eurographics 2003 - Short Presentations, Granada, Spain, September
1-5, 2003},
publisher = {Eurographics Association},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Blaise, Frédéric; Cavin, Xavier; Paul, Jean-Claude
High Performance Computing and Visualization for Forestry Applications - Project SILVES Proceedings Article
In: International Symposium on Plant growth Modeling, simulation, visualization and their Applications 2003 -PMA'03, pp. 194-202, Beijing, China, 2003, (Colloque avec actes et comité de lecture. internationale.).
@inproceedings{blaise:inria-00107687,
title = {High Performance Computing and Visualization for Forestry Applications - Project SILVES},
author = {Frédéric Blaise and Xavier Cavin and Jean-Claude Paul},
url = {https://inria.hal.science/inria-00107687},
year = {2003},
date = {2003-01-01},
booktitle = {International Symposium on Plant growth Modeling, simulation, visualization and their Applications 2003 -PMA'03},
pages = {194-202},
address = {Beijing, China},
note = {Colloque avec actes et comité de lecture. internationale.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Ray, Nicolas; Cavin, Xavier; Maigret, Bernard
Interactive Poster: Visualizing the Interaction Between Two Proteins Proceedings Article
In: IEEE Visualization 2003, IEEE, Seattle, United States, 2003, (Colloque avec actes et comité de lecture. internationale.).
@inproceedings{ray:inria-00107708,
title = {Interactive Poster: Visualizing the Interaction Between Two Proteins},
author = {Nicolas Ray and Xavier Cavin and Bernard Maigret},
url = {https://inria.hal.science/inria-00107708},
year = {2003},
date = {2003-01-01},
booktitle = {IEEE Visualization 2003},
publisher = {IEEE},
address = {Seattle, United States},
note = {Colloque avec actes et comité de lecture. internationale.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
2002
Thibault, Samuel; Cavin, Xavier; Festor, Olivier; Fleury, Eric
Unreliable Transport Protocol for Commodity-Based OpenGL Distributed Visualization Proceedings Article
In: Workshop on Commodity-Based Visualization Clusters, Boston, United States, 2002.
@inproceedings{thibault:inria-00363326,
title = {Unreliable Transport Protocol for Commodity-Based OpenGL Distributed Visualization},
author = {Samuel Thibault and Xavier Cavin and Olivier Festor and Eric Fleury},
url = {https://inria.hal.science/inria-00363326},
year = {2002},
date = {2002-10-01},
booktitle = {Workshop on Commodity-Based Visualization Clusters},
address = {Boston, United States},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Livnat, Yarden; Cavin, Xavier; Hansen, Charles
PHASE: Progressive Hardware Assisted IsoSurface Extraction Framework Technical Report
SCI Institute Technical Report no. UUSCI-2002-001, 2002.
Abstract | Links | BibTeX | Tags:
@techreport{Livnat2002,
title = {PHASE: Progressive Hardware Assisted IsoSurface Extraction Framework},
author = {Yarden Livnat and Xavier Cavin and Charles Hansen},
url = {https://www.sci.utah.edu/publications/yarden02/UUSCI-2002-001.pdf},
year = {2002},
date = {2002-06-30},
urldate = {2002-06-30},
booktitle = {SCI Institute Technical Report},
number = {UUSCI-2002-001},
institution = {SCI Institute Technical Report},
abstract = {Isosurface extraction is an important technique for visualizing three-dimensional scalar fields. During recent years, researchers have created many acceleration methods for isosurface extraction, including the span space representation and view-dependent methods. In this paper, wei ntroduce a progressive view-dependent isosurface extraction method that exhibits a rapid convergence rate to the exact isosurface and is well suited for remote visualization. The proposed method takes advantage of rendering hardware to resolve visibility tests. In contrast to previous view-dependent isosurface extraction methods, our method (PHASE) can quickly augment the current partial extracted isosurface based on a new point of view without the need for a full view-dependent extraction pass.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
Isosurface extraction is an important technique for visualizing three-dimensional scalar fields. During recent years, researchers have created many acceleration methods for isosurface extraction, including the span space representation and view-dependent methods. In this paper, wei ntroduce a progressive view-dependent isosurface extraction method that exhibits a rapid convergence rate to the exact isosurface and is well suited for remote visualization. The proposed method takes advantage of rendering hardware to resolve visibility tests. In contrast to previous view-dependent isosurface extraction methods, our method (PHASE) can quickly augment the current partial extracted isosurface based on a new point of view without the need for a full view-dependent extraction pass.
Cavin, Xavier; Hartner, Mark; Hansen, Charles
Implementation and Evaluation of Binary Swap Volume Rendering on a Commodity–Based Visualization Cluster Technical Report
School of Computing University of Utah 2002.
Abstract | Links | BibTeX | Tags:
@techreport{Cavin2002,
title = {Implementation and Evaluation of Binary Swap Volume Rendering on a Commodity–Based Visualization Cluster},
author = {Xavier Cavin and Mark Hartner and Charles Hansen},
url = {https://www.scalablegraphics.com/wp-content/uploads/2025/04/Implementation_and_Evaluation_of_Binary_Swap_Volum.pdf},
year = {2002},
date = {2002-06-30},
urldate = {2002-06-30},
institution = {School of Computing University of Utah},
abstract = { This paper describes the implementation and performance evaluation of a parallel volume renderer capable of handling large volumetric data sets. We implement our volume renderer on a cluster of 32 Linux PC’s using OpenGL, MPI and a binary–swap compositing algorithm. We also give hints for achieving good performance when using OpenGL and MPI on a Linux visualization cluster.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
This paper describes the implementation and performance evaluation of a parallel volume renderer capable of handling large volumetric data sets. We implement our volume renderer on a cluster of 32 Linux PC’s using OpenGL, MPI and a binary–swap compositing algorithm. We also give hints for achieving good performance when using OpenGL and MPI on a Linux visualization cluster.
Cavin, Xavier; Winkler, Christophe
High Performance Volumetric Data and Computational Field Visualization Proceedings Article
In: 22th gOcad Meeting, ASGA, 2002.
@inproceedings{CavinRM2002,
title = {High Performance Volumetric Data and Computational Field Visualization},
author = {Xavier Cavin and Christophe Winkler},
year = {2002},
date = {2002-06-01},
booktitle = {22th gOcad Meeting},
publisher = {ASGA},
abstract = {Today, volumetric data is produced by improving data acquisition techniques or by more and more efficient and complex physical phenomena simulations. As the amount of 3D data increases, the effectiveness of utilizing such high resolution data will hinge upon the ability of human experts to interact with their data and extract useful information. Visualization is one of the undeniable aspects of data analysis and manipulation. Here we describe recent work in large-scale scalar, vector, and tensor visualization techniques.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Today, volumetric data is produced by improving data acquisition techniques or by more and more efficient and complex physical phenomena simulations. As the amount of 3D data increases, the effectiveness of utilizing such high resolution data will hinge upon the ability of human experts to interact with their data and extract useful information. Visualization is one of the undeniable aspects of data analysis and manipulation. Here we describe recent work in large-scale scalar, vector, and tensor visualization techniques.
2001
Lévy, Bruno; Caumon, Guillaume; Conreaux, Stéphane; Cavin, Xavier
Circular Incident Edge Lists: A Data Structure for Rendering Complex Unstructured Grids Proceedings Article
In: Ertl, Thomas; Joy, Kenneth I.; Varshney, Amitabh (Ed.): 12th IEEE Visualization Conference, IEEE Vis 2001, San Diego, CA, USA, October 24-26, 2001, Proceedings, pp. 191–198, IEEE Computer Society, 2001.
@inproceedings{DBLP:conf/visualization/LevyCCC01,
title = {Circular Incident Edge Lists: A Data Structure for Rendering Complex
Unstructured Grids},
author = {Bruno Lévy and Guillaume Caumon and Stéphane Conreaux and Xavier Cavin},
editor = {Thomas Ertl and Kenneth I. Joy and Amitabh Varshney},
url = {https://doi.org/10.1109/VISUAL.2001.964511},
doi = {10.1109/VISUAL.2001.964511},
year = {2001},
date = {2001-01-01},
booktitle = {12th IEEE Visualization Conference, IEEE Vis 2001, San Diego,
CA, USA, October 24-26, 2001, Proceedings},
pages = {191–198},
publisher = {IEEE Computer Society},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Cavin, Xavier; Cuny, François
Real-time Visualization through the Internet Journal Article
In: ERCIM News, no. 44, pp. 29-30, 2001, (Article dans une revue de vulgarisation. nationale.).
@article{cavin:inria-00100490,
title = {Real-time Visualization through the Internet},
author = {Xavier Cavin and François Cuny},
url = {https://inria.hal.science/inria-00100490},
year = {2001},
date = {2001-01-01},
journal = {ERCIM News},
number = {44},
pages = {29-30},
publisher = {ERCIM},
note = {Article dans une revue de vulgarisation. nationale.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2000
Cavin, Xavier
Simulation numérique parallèle et graphisme haute-performance pour la synthèse d'images réalistes PhD Thesis
National Polytechnic Institute of Lorraine, Nancy, France, 2000.
@phdthesis{DBLP:phd/hal/Cavin00,
title = {Simulation numérique parallèle et graphisme haute-performance
pour la synthèse d'images réalistes},
author = {Xavier Cavin},
url = {https://hal.archives-ouvertes.fr/tel-01750387},
year = {2000},
date = {2000-01-01},
school = {National Polytechnic Institute of Lorraine, Nancy, France},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Cavin, Xavier; Paul, Jean-Claude; Alonso, Laurent
Partitioning and Scheduling Large Radiosity Computations in Parallel Journal Article
In: Parallel Distributed Comput. Pract., vol. 3, no. 3, 2000.
@article{DBLP:journals/scpe/CavinPA00,
title = {Partitioning and Scheduling Large Radiosity Computations in Parallel},
author = {Xavier Cavin and Jean-Claude Paul and Laurent Alonso},
url = {http://www.scpe.org/index.php/scpe/article/view/199},
year = {2000},
date = {2000-01-01},
journal = {Parallel Distributed Comput. Pract.},
volume = {3},
number = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cavin, Xavier; Alonso, Laurent
Parallel Management of Large Dynamic Shared Memory Space: A Hierarchical FEM Application Proceedings Article
In: Rolim, José D. P. (Ed.): Parallel and Distributed Processing, 15 IPDPS 2000 Workshops, Cancun, Mexico, May 1-5, 2000, Proceedings, pp. 428–434, Springer, 2000.
@inproceedings{DBLP:conf/ipps/CavinA00,
title = {Parallel Management of Large Dynamic Shared Memory Space: A Hierarchical
FEM Application},
author = {Xavier Cavin and Laurent Alonso},
editor = {José D. P. Rolim},
url = {https://doi.org/10.1007/3-540-45591-4_57},
doi = {10.1007/3-540-45591-4_57},
year = {2000},
date = {2000-01-01},
booktitle = {Parallel and Distributed Processing, 15 IPDPS 2000 Workshops, Cancun,
Mexico, May 1-5, 2000, Proceedings},
volume = {1800},
pages = {428–434},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Alonso, Laurent; Cavin, Xavier; Ulysse, Jean-Christophe; Paul, Jean-Claude
Fast and Accurate Wavelet Radiosity Computations Using High-End Platforms Proceedings Article
In: Girona, Universitat (Ed.): Third Eurographics Workshop on Parallel Graphics & Visualisation, pp. 25–38, Girona, Spain, 2000, (Colloque avec actes et comité de lecture. internationale.).
@inproceedings{alonso:inria-00099037,
title = {Fast and Accurate Wavelet Radiosity Computations Using High-End Platforms},
author = {Laurent Alonso and Xavier Cavin and Jean-Christophe Ulysse and Jean-Claude Paul},
editor = {Universitat Girona},
url = {https://inria.hal.science/inria-00099037},
year = {2000},
date = {2000-01-01},
booktitle = {Third Eurographics Workshop on Parallel Graphics & Visualisation},
pages = {25–38},
address = {Girona, Spain},
note = {Colloque avec actes et comité de lecture. internationale.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
1999
Cavin, Xavier; Alonso, Laurent; Paul, Jean-Claude
Overlapping multi-processing and graphics hardware acceleration: performance evaluation Proceedings Article
In: Ahrens, James P.; Chalmers, Alan; Shen, Han-Wei (Ed.): Proceedings of the 1999 IEEE Symposium on Parallel Visualization and Graphics, PVGS 1999, San Francisco, California, USA, October 25-26, 1999, pp. 79–88, IEEE Computer Society, 1999.
@inproceedings{DBLP:conf/pvgs/CavinAP99,
title = {Overlapping multi-processing and graphics hardware acceleration: performance
evaluation},
author = {Xavier Cavin and Laurent Alonso and Jean-Claude Paul},
editor = {James P. Ahrens and Alan Chalmers and Han-Wei Shen},
url = {https://doi.org/10.1145/328712.319340},
doi = {10.1145/328712.319340},
year = {1999},
date = {1999-01-01},
booktitle = {Proceedings of the 1999 IEEE Symposium on Parallel Visualization
and Graphics, PVGS 1999, San Francisco, California, USA, October
25-26, 1999},
pages = {79–88},
publisher = {IEEE Computer Society},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Winkler, Christophe; Bosquet, Fabien; Cavin, Xavier; Paul, Jean-Claude
Design and Implementation of an Immersive Geoscience Toolkit Proceedings Article
In: Ebert, David S.; Gross, Markus H.; Hamann, Bernd (Ed.): 10th IEEE Visualization Conference, IEEE Vis 1999, San Francisco, CA, USA, October 24-29, 1999, Proceedings, pp. 429–432, IEEE Computer Society and ACM, 1999.
@inproceedings{DBLP:conf/visualization/WinklerBCP99,
title = {Design and Implementation of an Immersive Geoscience Toolkit},
author = {Christophe Winkler and Fabien Bosquet and Xavier Cavin and Jean-Claude Paul},
editor = {David S. Ebert and Markus H. Gross and Bernd Hamann},
url = {https://doi.org/10.1109/VISUAL.1999.809922},
doi = {10.1109/VISUAL.1999.809922},
year = {1999},
date = {1999-01-01},
booktitle = {10th IEEE Visualization Conference, IEEE Vis 1999, San Francisco,
CA, USA, October 24-29, 1999, Proceedings},
pages = {429–432},
publisher = {IEEE Computer Society and ACM},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Cavin, Xavier
Load Balancing Analysis of a Parallel Hierarchical Algorithm on the Origin2000 Proceedings Article
In: Fifth European SGI/Cray MPP Workshop, pp. 10 p, CINECA Bologna, Italy, 1999, (Colloque avec actes sans comité de lecture.).
@inproceedings{cavin:inria-00107796,
title = {Load Balancing Analysis of a Parallel Hierarchical Algorithm on the Origin2000},
author = {Xavier Cavin},
url = {https://inria.hal.science/inria-00107796},
year = {1999},
date = {1999-01-01},
booktitle = {Fifth European SGI/Cray MPP Workshop},
pages = {10 p},
address = {Bologna, Italy},
organization = {CINECA},
note = {Colloque avec actes sans comité de lecture.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
1998
Cavin, Xavier; Alonso, Laurent; Paul, Jean-Claude
Experimentation of Data Locality Performance for a Parallel Hierarchical Algorithm on the Origin2000 Proceedings Article
In: Fourth European CRAY-SGI MPP Workshop, pp. 178-187, IPP, Garching/Munich, Germany, 1998, (Colloque avec actes et comité de lecture.).
@inproceedings{cavin:inria-00098705,
title = {Experimentation of Data Locality Performance for a Parallel Hierarchical Algorithm on the Origin2000},
author = {Xavier Cavin and Laurent Alonso and Jean-Claude Paul},
url = {https://inria.hal.science/inria-00098705},
year = {1998},
date = {1998-01-01},
booktitle = {Fourth European CRAY-SGI MPP Workshop},
volume = {R/46},
number = {R/46},
pages = {178-187},
publisher = {IPP},
address = {Garching/Munich, Germany},
note = {Colloque avec actes et comité de lecture.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Cavin, Xavier; Alonso, Laurent; Paul, Jean-Claude
Parallel Wavelet Radiosity Proceedings Article
In: Bouatouch, Kadi; Chalmers, Alan; Priol, Thierry (Ed.): Proceedings of the Second Eurographics Workshop on Parallel Graphics and Visualisation, pp. 61-75, Rennes, France, 1998, (Colloque avec actes et comité de lecture.).
@inproceedings{cavin:inria-00098703,
title = {Parallel Wavelet Radiosity},
author = {Xavier Cavin and Laurent Alonso and Jean-Claude Paul},
editor = {Kadi Bouatouch and Alan Chalmers and Thierry Priol},
url = {https://inria.hal.science/inria-00098703},
year = {1998},
date = {1998-01-01},
booktitle = {Proceedings of the Second Eurographics Workshop on Parallel Graphics and Visualisation},
pages = {61-75},
address = {Rennes, France},
note = {Colloque avec actes et comité de lecture.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
1996
Cavin, Xavier
Intersections de surfaces triangulées : amélioration du maillage. Masters Thesis
Henri Poincaré University of Nancy, 1996.
BibTeX | Tags:
@mastersthesis{Cavin1996,
title = {Intersections de surfaces triangulées : amélioration du maillage.},
author = {Xavier Cavin},
year = {1996},
date = {1996-09-30},
school = {Henri Poincaré University of Nancy},
keywords = {},
pubstate = {published},
tppubtype = {mastersthesis}
}
Cavin, Xavier
An approach for a «cut beautifier» Proceedings Article
In: 13th gOcad Meeting, ASGA, 1996.
@inproceedings{CavinRM1996a,
title = {An approach for a «cut beautifier»},
author = {Xavier Cavin},
year = {1996},
date = {1996-06-01},
booktitle = {13th gOcad Meeting},
publisher = {ASGA},
abstract = {We present a new way for beautifying border triangles resulting, for example, from intersection operations between surfaces. We first present the algoritm we have developed for beautifying surfaces borders. We show then the application of this algorithm to cut frontiers and we finally expose the further step to a «light» cut, able to directly produce beautiful triangles.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
We present a new way for beautifying border triangles resulting, for example, from intersection operations between surfaces. We first present the algoritm we have developed for beautifying surfaces borders. We show then the application of this algorithm to cut frontiers and we finally expose the further step to a «light» cut, able to directly produce beautiful triangles.
1995
Filbois, Alain
Institut National Polytechnique de Lorraine, 1995, (Texte intégral accessible uniquement aux membres de l'Université de Lorraine).
@phdthesis{filbois:tel-01751594,
title = {Contributions à la modélisation automatique d'objets polyédriques 3D : extraction des primitives 3D, facettes et segments},
author = {Alain Filbois},
url = {https://hal.univ-lorraine.fr/tel-01751594},
year = {1995},
date = {1995-07-01},
number = {1995INPL075N},
school = {Institut National Polytechnique de Lorraine},
note = {Texte intégral accessible uniquement aux membres de l'Université de Lorraine},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
1994
Filbois, Alain; Gemmerlé, Didier
From Step Edge to Line Edge: Combining Geometric and Photometric Information Proceedings Article
In: Proceedings of MVA '94 IAPR Workshop on machine vision application, pp. 87-90, IAPR MVA'94 Committee, Kawasaki, Japan, 1994.
@inproceedings{filbois:hal-03767430,
title = {From Step Edge to Line Edge: Combining Geometric and Photometric Information},
author = {Alain Filbois and Didier Gemmerlé},
url = {https://hal.science/hal-03767430},
year = {1994},
date = {1994-12-01},
booktitle = {Proceedings of MVA '94 IAPR Workshop on machine vision application},
pages = {87-90},
publisher = {IAPR MVA'94 Committee},
address = {Kawasaki, Japan},
series = {Proceedings of MVA '94 IAPR Workshop on machine vision application},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Gemmerlé, Didier; Filbois, Alain
Cooperation of 3D segments and 3D facets information for object reconstruction Proceedings Article
In: MVA'94 IAPR Workshop on Machine Vision Applications, Kawasaki, Japan, 1994.
@inproceedings{gemmerle:hal-03767444,
title = {Cooperation of 3D segments and 3D facets information for object reconstruction},
author = {Didier Gemmerlé and Alain Filbois},
url = {https://hal.science/hal-03767444},
year = {1994},
date = {1994-12-01},
booktitle = {MVA'94 IAPR Workshop on Machine Vision Applications},
address = {Kawasaki, Japan},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Gemmerlé, Didier; Filbois, Alain; Chabbi, Houda
Construction of 3D Views from Strereoscopic Triplet of Images Proceedings Article
In: Proceedings of 1st International Conference on Image Processing, pp. 715-719, IEEE, Austin, United States, 1994.
@inproceedings{gemmerle:hal-03766959,
title = {Construction of 3D Views from Strereoscopic Triplet of Images},
author = {Didier Gemmerlé and Alain Filbois and Houda Chabbi},
url = {https://hal.science/hal-03766959},
doi = {10.1109/ICIP.1994.413664},
year = {1994},
date = {1994-11-01},
booktitle = {Proceedings of 1st International Conference on Image Processing},
volume = {2},
pages = {715-719},
publisher = {IEEE},
address = {Austin, United States},
series = {ICIP'94: Proceedings of 1th IEEE International Conference on Image Processing},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Recent Comments