Browsing by Author "Veltkamp, Remco C."

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    Classification in Cryo-Electron Tomograms
    (The Eurographics Association, 2019) Gubins, Ilja; Schot, Gijs van der; Veltkamp, Remco C.; Förster, Friedrich; Du, Xuefeng; Zeng, Xiangrui; Zhu, Zhenxi; Chang, Lufan; Xu, Min; Moebel, Emmanuel; Martinez-Sanchez, Antonio; Kervrann, Charles; Lai, Tuan M.; Han, Xusi; Terashi, Genki; Kihara, Daisuke; Himes, Benjamin A.; Wan, Xiaohua; Zhang, Jingrong; Gao, Shan; Hao, Yu; Lv, Zhilong; Wan, Xiaohua; Yang, Zhidong; Ding, Zijun; Cui, Xuefeng; Zhang, Fa; Biasotti, Silvia and Lavoué, Guillaume and Veltkamp, Remco
    Different imaging techniques allow us to study the organization of life at different scales. Cryo-electron tomography (cryo-ET) has the ability to three-dimensionally visualize the cellular architecture as well as the structural details of macro-molecular assemblies under near-native conditions. Due to beam sensitivity of biological samples, an inidividual tomogram has a maximal resolution of 5 nanometers. By averaging volumes, each depicting copies of the same type of a molecule, resolutions beyond 4 Ă… have been achieved. Key in this process is the ability to localize and classify the components of interest, which is challenging due to the low signal-to-noise ratio. Innovation in computational methods remains key to mine biological information from the tomograms. To promote such innovation, we organize this SHREC track and provide a simulated dataset with the goal of establishing a benchmark in localization and classification of biological particles in cryo-electron tomograms. The publicly available dataset contains ten reconstructed tomograms obtained from a simulated cell-like volume. Each volume contains twelve different types of proteins, varying in size and structure. Participants had access to 9 out of 10 of the cell-like ground-truth volumes for learning-based methods, and had to predict protein class and location in the test tomogram. Five groups submitted eight sets of results, using seven different methods. While our sample size gives only an anecdotal overview of current approaches in cryo-ET classification, we believe it shows trends and highlights interesting future work areas. The results show that learning-based approaches is the current trend in cryo-ET classification research and specifically end-to-end 3D learning-based approaches achieve the best performance.
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    Eurographics Workshop on 3D Object Retrieval - Short Papers: Frontmatter
    (The Eurographics Association, 2022) Berretti, Stefano; Thehoaris, Theoharis; Daoudi, Mohamed; Ferrari, Claudio; Veltkamp, Remco C.; Berretti, Stefano; Thehoaris, Theoharis; Daoudi, Mohamed; Ferrari, Claudio; Veltkamp, Remco C.
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    Eurographics Workshop on 3D Object Retrieval - Short Papers: Frontmatter
    (The Eurographics Association, 2023) Fugacci, Ulderico; Lavoué, Guillaume; Veltkamp, Remco C.; Fugacci, Ulderico; Lavoué, Guillaume; Veltkamp, Remco C.
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    Eurographics Workshop on 3D Object Retrieval: Short Papers Frontmatter
    (The Eurographics Association, 2021) Biasotti, Silvia; Dyke, Roberto M.; Lai, Yukun; Rosin, Paul L.; Veltkamp, Remco C.; Biasotti, Silvia and Dyke, Roberto M. and Lai, Yukun and Rosin, Paul L. and Veltkamp, Remco C.
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    Eurographics Workshop on 3D Object Retrieval: Short Papers Frontmatter
    (The Eurographics Association, 2020) Schreck, Tobias; Theoharis, Theoharis; Pratikakis, Ioannis; Spagnuolo, Michela; Veltkamp, Remco C.; Schreck, Tobias and Theoharis, Theoharis and Pratikakis, Ioannis and Spagnuolo, Michela and Veltkamp, Remco C.
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    SHREC 2020 Track: 6D Object Pose Estimation
    (The Eurographics Association, 2020) Yuan, Honglin; Veltkamp, Remco C.; Albanis, Georgios; Zioulis, Nikolaos; Zarpalas, Dimitrios; Daras, Petros; Schreck, Tobias and Theoharis, Theoharis and Pratikakis, Ioannis and Spagnuolo, Michela and Veltkamp, Remco C.
    6D pose estimation is crucial for augmented reality, virtual reality, robotic manipulation and visual navigation. However, the problem is challenging due to the variety of objects in the real world. They have varying 3D shape and their appearances in captured images are affected by sensor noise, changing lighting conditions and occlusions between objects. Different pose estimation methods have different strengths and weaknesses, depending on feature representations and scene contents. At the same time, existing 3D datasets that are used for data-driven methods to estimate 6D poses have limited view angles and low resolution. To address these issues, we organize the Shape Retrieval Challenge benchmark on 6D pose estimation and create a physically accurate simulator that is able to generate photo-realistic color-and-depth image pairs with corresponding ground truth 6D poses. From captured color and depth images, we use this simulator to generate a 3D dataset which has 400 photo-realistic synthesized color-and-depth image pairs with various view angles for training, and another 100 captured and synthetic images for testing. Five research groups register in this track and two of them submitted their results. Data-driven methods are the current trend in 6D object pose estimation and our evaluation results show that approaches which fully exploit the color and geometric features are more robust for 6D pose estimation of reflective and texture-less objects and occlusion. This benchmark and comparative evaluation results have the potential to further enrich and boost the research of 6D object pose estimation and its applications.
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    SHREC 2021: Classification in Cryo-electron Tomograms
    (The Eurographics Association, 2021) Gubins, Ilja; Chaillet, Marten L.; Schot, Gijs van der; Trueba, M. Cristina; Veltkamp, Remco C.; Förster, Friedrich; Wang, Xiao; Kihara, Daisuke; Moebel, Emmanuel; Nguyen, Nguyen P.; White, Tommi; Bunyak, Filiz; Papoulias, Giorgos; Gerolymatos, Stavros; Zacharaki, Evangelia I.; Moustakas, Konstantinos; Zeng, Xiangrui; Liu, Sinuo; Xu, Min; Wang, Yaoyu; Chen, Cheng; Cui, Xuefeng; Zhang, Fa; Biasotti, Silvia and Dyke, Roberto M. and Lai, Yukun and Rosin, Paul L. and Veltkamp, Remco C.
    Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and inability to obtain images from all angles. Computational methods are key to analyze cryo-electron tomograms. To promote innovation in computational methods, we generate a novel simulated dataset to benchmark different methods of localization and classification of biological macromolecules in tomograms. Our publicly available dataset contains ten tomographic reconstructions of simulated cell-like volumes. Each volume contains twelve different types of complexes, varying in size, function and structure. In this paper, we have evaluated seven different methods of finding and classifying proteins. Seven research groups present results obtained with learning-based methods and trained on the simulated dataset, as well as a baseline template matching (TM), a traditional method widely used in cryo-ET research. We show that learning-based approaches can achieve notably better localization and classification performance than TM. We also experimentally confirm that there is a negative relationship between particle size and performance for all methods.