SHREC 2021: Classification in cryo-electron tomograms

Authors:
  • IGIlja Gubins
    Ilja Gubins
  • MCMarten L. Chaillet
    Marten L. Chaillet
  • GSGijs van der Schot
    Gijs van der Schot
  • MTM. Cristina Trueba
    M. Cristina Trueba
  • RVRemco C. Veltkamp
    Remco C. Veltkamp
  • FFFriedrich Förster
    Friedrich Förster
  • XWXiao Wang
    Xiao Wang
  • DKDaisuke Kihara
    Daisuke Kihara
  • EMEmmanuel Moebel
    Emmanuel Moebel
  • NNNguyen P. Nguyen
    Nguyen P. Nguyen
  • TWTommi White
    Tommi White
  • FBFiliz Bunyak
    Filiz Bunyak
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Abstract
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.
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