Xiaohua Wan

Ilja Gubins, Marten L. Chaillet, Gijs van der Schot et al.

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.

Enze Zhang, Fa Zhang, Zhiyong Liu et al.

Electron tomography (ET) allows high-resolution reconstructions of macromolecular complexes at nearnative state. Cellular structures segmentation in the reconstruction data from electron tomographic images is often required for analyzing and visualizing biological structures, making it a powerful tool for quantitative descriptions of whole cell structures and understanding biological functions. However, these cellular structures are rather difficult to automatically separate or quantify from view owing to complex molecular environment and the limitations of reconstruction data of ET. In this paper, we propose a single end-to-end deep fully-convolutional semantic segmentation network dubbed SegET with rich contextual features which fully exploitsthe multi-scale and multi-level contextual information and reduces the loss of details of cellular structures in ET images. We trained and evaluated our network on the electron tomogram of the CTL Immunological Synapse from Cell Image library. Our results demonstrate that SegET can automatically segment accurately and outperform all other baseline methods on each individual structure in our ET dataset.