Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation
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Main article
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Author(s)
Pintilie, Grigore Dimitrie
Zhang, Junjie
Chiu, Wah
Gossard, David C.
Date Issued
April 2009
Journal
IEEE/NIH Life Science Systems and Applications Workshop
Publisher
Institute of Electrical and Electronics Engineers
Citation
Pintilie, Grigore Dimitrie et al. “Identifying components in 3D density maps of protein nanomachines by multi-scale segmentation.” IEEE/NIH Life Science Systems and Applications Workshop. 2009. 44-47.
Version
Final published version
Abstract
Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive interactive methods. The goal of segmentation is to identify the regions inside the density map that correspond to individual components. We present a multi-scale segmentation method for accomplishing this task that requires very little user interaction. The method uses the concept of scale space, which is created by convolution of the input density map with a Gaussian filter. The latter process smoothes the density map. The standard deviation of the Gaussian filter is varied, with smaller values corresponding to finer scales and larger values to coarser scales. Each of the maps at different scales is segmented using the watershed method, which is very efficient, completely automatic, and does not require the specification of seed points. Some detail is lost in the smoothing process. A sharpening process reintroduces detail into the segmentation at the coarsest scale by using the segmentations at the finer scales. We apply the method to simulated density maps, where the exact segmentation (or ground truth) is known, and rigorously evaluate the accuracy of the resulting segmentations.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology. Department of Mechanical Engineering
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
http://dx.doi.org/10.1109/LISSA.2009.4906705
