Automated identification of filaments in cryoelectron microscopy images.

Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large numbers of images--one of the critical steps toward the reconstruction at high resolution--is still constrained by manual processing even though interactive interfaces have been built to aid the tedious and sometimes inaccurate boxing process. This article describes an accurate approach for automated detection of filamentous structures in low-contrast images acquired in defocus pairs using cryoelectron microscopy. The performance of the approach has been evaluated across various magnifications and at a series of defocus values using tobacco mosaic virus (TMV) preserved in vitreous ice as a test specimen. By integrating the proposed approach into our automated data acquisition and reconstruction system, we are now able to generate a three-dimensional map of TMV to approximately 10-A resolution within 24 h of inserting the specimen grid into the microscope.

What shadows reveal about object structure.

In a scene observed from a fixed viewpoint, the set of shadow boundaries in an image changes as a point light source (nearby or at infinity) assumes different locations. We show that for any finite set of point light sources illuminating an object viewed under either orthographic or perspective projection, there is an equivalence class of object shapes having the same set of shadows. Members of this equivalence class differ by a four-parameter family of projective transformations, and the shadows of a transformed object are identical when the same transformation is applied to the light source locations. Under orthographic projection, this family is the generalized bas-relief (GBR) transformation, and we show that the GBR transformation is the only family of transformations of an object's shape for which the complete set of imaged shadows is identical. Finally, we show that given multiple images under differing and unknown light source directions, it is possible to reconstruct both an object's surface and the light source locations up to this family of transformations from the shadows alone.

What defines a view?

At a given instant we see only visible surfaces, not an object's complete 3D appearance. Thus, objects may be represented as discrete 'views' showing only those features visible from a limited range of viewpoints. We address how to define a view using Koenderink's (Koenderink & Van Doorn, Biol. Cybernet. 32 (1979) 211.) geometric method for enumerating complete sets of stable views as aspect graphs. Using objects with known aspect graphs, five experiments examined whether the perception of orientation is sensitive to the qualitative features that define aspect graphs. Highest sensitivity to viewpoint changes was observed at locations where the theory predicts qualitative transitions, although some transitions did not affect performance. Hypotheses about why humans ignore some transitions offer insights into mechanisms for object representation.