Classification in Cryo-Electron Tomograms

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; Yang, Zhidong; Ding, Zijun; Cui, Xuefeng; Zhang, Fa

Classification in Cryo-Electron Tomograms

Files

049-054.pdf (529.79 KB)

Date

2019

Publisher

The Eurographics Association

Abstract

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 Å 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.

        @inproceedings{10.2312:3dor.20191061
,
booktitle = {Eurographics Workshop on 3D Object Retrieval
},
editor = {Biasotti, Silvia and Lavoué, Guillaume and Veltkamp, Remco
},
title = {{Classification in Cryo-Electron Tomograms
}},
author = {Gubins, Ilja and 
Schot, Gijs van der and 
Martinez-Sanchez, Antonio and 
Kervrann, Charles and 
Lai, Tuan M. and 
Han, Xusi and 
Terashi, Genki and 
Kihara, Daisuke and 
Himes, Benjamin A. and 
Wan, Xiaohua and 
Zhang, Jingrong and 
Gao, Shan and 
Veltkamp, Remco C. and 
Hao, Yu and 
Lv, Zhilong and 
Wan, Xiaohua and 
Yang, Zhidong and 
Ding, Zijun and 
Cui, Xuefeng and 
Zhang, Fa and 
Förster, Friedrich and 
Du, Xuefeng and 
Zeng, Xiangrui and 
Zhu, Zhenxi and 
Chang, Lufan and 
Xu, Min and 
Moebel, Emmanuel
},
year = {2019
},
publisher = {The Eurographics Association
},
ISSN = {1997-0471
},
ISBN = {978-3-03868-077-2
},
DOI = {10.2312/3dor.20191061
}
}