75 research outputs found
Alignment of cryo-EM movies of individual particles by optimization of image translations
Direct detector device (DDD) cameras have revolutionized single particle
electron cryomicroscopy (cryo-EM). In addition to an improved camera detective
quantum efficiency, acquisition of DDD movies allows for correction of movement
of the specimen, due both to instabilities in the microscope specimen stage and
electron beam-induced movement. Unlike specimen stage drift, beam-induced
movement is not always homogeneous within an image. Local correlation in the
trajectories of nearby particles suggests that beam-induced motion is due to
deformation of the ice layer. Algorithms have already been described that can
correct movement for large regions of frames and for > 1 MDa protein particles.
Another algorithm allows individual < 1 MDa protein particle trajectories to be
estimated, but requires rolling averages to be calculated from frames and fits
linear trajectories for particles. Here we describe an algorithm that allows
for individual < 1 MDa particle images to be aligned without frame averaging or
linear trajectories. The algorithm maximizes the overall correlation of the
shifted frames with the sum of the shifted frames. The optimum in this single
objective function is found efficiently by making use of analytically
calculated derivatives of the function. To smooth estimates of particle
trajectories, rapid changes in particle positions between frames are penalized
in the objective function and weighted averaging of nearby trajectories ensures
local correlation in trajectories. This individual particle motion correction,
in combination with weighting of Fourier components to account for increasing
radiation damage in later frames, can be used to improve 3-D maps from single
particle cryo-EM.Comment: 11 pages, 4 figure
Building Proteins in a Day: Efficient 3D Molecular Reconstruction
Discovering the 3D atomic structure of molecules such as proteins and viruses
is a fundamental research problem in biology and medicine. Electron
Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure
estimation which attempts to reconstruct 3D structures from 2D images. This
paper addresses the challenging problem of 3D reconstruction from 2D Cryo-EM
images. A new framework for estimation is introduced which relies on modern
stochastic optimization techniques to scale to large datasets. We also
introduce a novel technique which reduces the cost of evaluating the objective
function during optimization by over five orders or magnitude. The net result
is an approach capable of estimating 3D molecular structure from large scale
datasets in about a day on a single workstation.Comment: To be presented at IEEE Conference on Computer Vision and Pattern
Recognition (CVPR) 201
Find your Way by Observing the Sun and Other Semantic Cues
In this paper we present a robust, efficient and affordable approach to
self-localization which does not require neither GPS nor knowledge about the
appearance of the world. Towards this goal, we utilize freely available
cartographic maps and derive a probabilistic model that exploits semantic cues
in the form of sun direction, presence of an intersection, road type, speed
limit as well as the ego-car trajectory in order to produce very reliable
localization results. Our experimental evaluation shows that our approach can
localize much faster (in terms of driving time) with less computation and more
robustly than competing approaches, which ignore semantic information
- …