Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm
Document Type
Article
Publication Date
2013
DOI
10.1109/TCBB.2013.121
Publication Title
IEEE-ACM Transactions on Computational Biology and Bioinformatics
Volume
10
Issue
5
Pages
1289-1298
Abstract
Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the image can be captured using a single segmentation. In this paper, we present a segmentation-free approach to extract the gray-scale curve-like skeletons. The approach relies on a novel representation of the 3D image, where the image is modeled as a graph and a set of volume trees. A test containing 36 synthesized maps and one authentic map shows that our approach can improve the performance of the two tested tools used in de novo modeling. The improvements were 62 and 13 percent for Gorgon and DP-TOSS, respectively.
Original Publication Citation
Al Nasr, K., Liu, C. M., Rwebangira, M., Burge, L., & He, J. (2013). Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 10(5), 1289-1298. doi:10.1109/tcbb.2013.121
Repository Citation
Al Nasr, K., Liu, C. M., Rwebangira, M., Burge, L., & He, J. (2013). Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 10(5), 1289-1298. doi:10.1109/tcbb.2013.121
Included in
Biochemistry Commons, Computer Sciences Commons, Mathematics Commons
Comments
NOTE: This is the author's post-print version of a work that was published in IEEE-ACM Transactions on Computational Biology and Bioinformatics. The final version was published as:
Al Nasr, K., Liu, C. M., Rwebangira, M., Burge, L., & He, J. (2013). Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 10(5), 1289-1298. doi:10.1109/tcbb.2013.121
Available at: http://dx.doi.org/10.1109/tcbb.2013.121