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dc.contributor.authorLiu, Sinuo
dc.contributor.authorBan, Xiaojuan
dc.contributor.authorZeng, Xiangrui
dc.contributor.authorZhao, Fengnian
dc.contributor.authorGao, Yuan
dc.contributor.authorWu, Wenjie
dc.contributor.authorZhang, Hongpan
dc.contributor.authorChen, Feiyang
dc.contributor.authorHall, Thomas
dc.contributor.authorGao, Xin
dc.contributor.authorXu, Min
dc.date.accessioned2020-09-17T08:18:01Z
dc.date.available2020-09-17T08:18:01Z
dc.date.issued2020
dc.identifier.citationSinuo Liu, Xiaojuan Ban, Xiangrui Zeng, Fengnian Zhao, Gao, Y., Wenjie Wu, Hongpan Zhang, Feiyang Chen, Hall, T., Gao, X., & Xu, M. (2020). A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.5116764
dc.identifier.doi10.6084/m9.figshare.c.5116764
dc.identifier.urihttp://hdl.handle.net/10754/665210
dc.description.abstractAbstract Background Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecular complexes in a sample cell. However, due to the compact and crowded status, the missing edge effect, and low signal to noise ratio (SNR), it is extremely challenging to recover such information with existing image processing methods. Cryo-electron tomogram simulation is an effective solution to test and optimize the performance of the above image processing methods. The simulated images could be regarded as the labeled data which covers a wide range of macromolecular complexes and ultrastructure. To approximate the crowded cellular environment, it is very important to pack these heterogeneous structures as tightly as possible. Besides, simulating non-deformable and deformable components under a unified framework also need to be achieved. Result In this paper, we proposed a unified framework for simulating crowded cryo-electron tomogram images including non-deformable macromolecular complexes and deformable ultrastructures. A macromolecule was approximated using multiple balls with fixed relative positions to reduce the vacuum volume. A ultrastructure, such as membrane and filament, was approximated using multiple balls with flexible relative positions so that this structure could deform under force field. In the experiment, 400 macromolecules of 20 representative types were packed into simulated cytoplasm by our framework, and numerical verification proved that our method has a smaller volume and higher compression ratio than the baseline single-ball model. We also packed filaments, membranes and macromolecules together, to obtain a simulated cryo-electron tomogram image with deformable structures. The simulated results are closer to the real Cryo-ET, making the analysis more difficult. The DOG particle picking method and the image segmentation method are tested on our simulation data, and the experimental results show that these methods still have much room for improvement. Conclusion The proposed multi-ball model can achieve more crowded packaging results and contains richer elements with different properties to obtain more realistic cryo-electron tomogram simulation. This enables users to simulate cryo-electron tomogram images with non-deformable macromolecular complexes and deformable ultrastructures under a unified framework. To illustrate the advantages of our framework in improving the compression ratio, we calculated the volume of simulated macromolecular under our multi-ball method and traditional single-ball method. We also performed the packing experiment of filaments and membranes to demonstrate the simulation ability of deformable structures. Our method can be used to do a benchmark by generating large labeled cryo-ET dataset and evaluating existing image processing methods. Since the content of the simulated cryo-ET is more complex and crowded compared with previous ones, it will pose a greater challenge to existing image processing methods.
dc.publisherfigshare
dc.subjectArtificial Intelligence and Image Processing
dc.subjectFOS: Computer and information sciences
dc.subjectFOS: Computer and information sciences
dc.titleA unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation
dc.typeDataset
dc.contributor.departmentKing Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia.
dc.contributor.institutionBeijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China.
dc.contributor.institutionComputational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States.
dc.contributor.institutionWuYuzhang Honors College, Sichuan University, Sichuan, China.
dc.contributor.institutionorgnameSchool of Computer Science, Beijing University of Posts and Telecommunications, Beijing, China.
dc.contributor.institutionSchool of Information Science and Technology, Beijing Forestry University, Beijing, China.
dc.contributor.institutionCollege of Life Science, Sichuan University, Sichuan, China
dc.contributor.institutionSchool of Mechanical, Electrical and Information Engineering, Shandong University, Shandong, China.
kaust.personChen, Feiyang
dc.relation.issupplementtoDOI:10.1186/s12859-020-03660-w
display.relations<b> Is Supplement To:</b><br/> <ul> <li><i>[Article]</i> <br/> Liu, S., Ban, X., Zeng, X., Zhao, F., Gao, Y., Wu, W., … Xu, M. (2020). A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation. BMC Bioinformatics, 21(1). doi:10.1186/s12859-020-03660-w. DOI: <a href="https://doi.org/10.1186/s12859-020-03660-w" >10.1186/s12859-020-03660-w</a> HANDLE: <a href="http://hdl.handle.net/10754/665088">10754/665088</a></li></ul>


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