Segmentation and registration of molecular components in 3-dimensional density maps from cryo-electron microscopy

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 89-93).Cryo-electron microscopy is a method that produces 3D density maps of macromolecular complexes. Segmentation and registration methods are heavily used to extract structural information from such density maps. Segmentation aims to identify regions in a density map corresponding to individual molecular components, so as to allow us to understand their complex arrangements and the relation of these arrangements to the function of the complex. Currently used segmentation methods rely to a large degree upon user interaction and thus are tedious and yield subjective results. We present a multi-scale segmentation method requiring very little interaction and guidance from the user. The segmentation accuracy of this method is quantified for simulated density maps, using a shape-based metric. The method is applied to several density maps of various sizes and complexity, producing accurate results. Registration of molecular structures with density maps helps to relate the vast structural information from X-ray crystallography with the structural information contained in cryo-electron microscopy density maps. The most reliable registration methods to date depend on exhaustive search, which is time-intensive and scales poorly with map and structure size. Two methods are presented that achieve direct registration of structures with density maps, based on the alignment of the structures to segmented regions.(cont.) The registrations are refined using a gradient-based method, which locally optimizes the density cross-correlation score. A search algorithm is presented for automatically finding groups of regions that produce correct registrations. The accuracy of these registration methods is measured using simulated density maps, and then the methods are used to register structures of individual proteins and subunits with density maps obtained by cryo-electron microscopy.by Grigore D. Pintilie.Ph.D

Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation

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

Interactive cutting of surface meshes for computer-aided surgical planning

grantor: University of TorontoThe goal of a computer-aided surgery planning system is to allow surgeons to plan surgical operations in a virtual environment, aided by realistic visual and haptic feedback. In this thesis we develop such a system, building upon commercial medical image analysis software and a versatile haptic input/output device. In our system we have implemented cutting and positioning operations supported by realistic haptic and graphic feedback. We also present algorithms for making template planar cuts and free-hand contour cuts through solid objects represented by triangular surface meshes. Mesh-cutting algorithms are complicated because they require the mesh topology to be changed, and this may introduce degenerate mesh elements. The algorithms we develop introduce approximation and mesh refinement approaches to eliminate mesh degeneracies due to cutting operations, and a sampling technique that yields predictable cut accuracy independent of the mesh structure.M.Sc