Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.

Abstract. In this work, we present a method to uncover shape from webcams "in the wild." We present a variant of photometric stereo which uses the sun as a distant light source, so that lighting direction can be computed from known GPS and timestamps. We propose an iterative, non-linear optimization process that optimizes the error in reproducing all images from an extended time-lapse with an image formation model that accounts for ambient lighting, shadows, changing light color, dense surface normal maps, radiometric calibration, and exposure. Unlike many approaches to uncalibrated outdoor image analysis, this procedure is automatic, and we report quantitative results by comparing extracted surface normals to Google Earth 3D models. We evaluate this procedure on data from a varied set of scenes and emphasize the advantages of including imagery from many months.

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Shadows encode a powerful geometric cue: if one pixel casts a shadow onto another, then the two pixels are colinear with the lighting direction. Given many images over many lighting directions, this constraint can be leveraged to recover the depth of a scene from a single viewpoint. For outdoor scenes with solar illumination, we term this the episolar constraint, which provides a convex optimization to solve for the sparse depth of a scene from shadow correspondences, a method to reduce the search space when finding shadow correspondences, and a method to geometrically calibrate a camera using shadow constraints. Our method constructs a dense network of nonlocal constraints which complements recent work on outdoor photometric stereo and cloud based cues for 3D. We demonstrate results across a variety of time-lapse sequences from webcams "in the wild."

Abstract-We describe algorithms that use cloud shadows as a form of stochastically structured light to support 3D scene geometry estimation. Taking video captured from a static outdoor camera as input, we use the relationship of the time series of intensity values between pairs of pixels as the primary input to our algorithms. We describe two cues that relate the 3D distance between a pair of points to the pair of intensity time series. The first cue results from the fact that two pixels that are nearby in the world are more likely to be under a cloud at the same time than two distant clouds. We describe methods for using this cue to estimate focal length and scene structure. The second cue is based on the motion of shadow clouds across the scene; this cue results in a set of linear constraints on scene structure. These constraints have an inherent ambiguity, which we show how to overcome by combining the cloud motion cue with the spatial cue. We evaluate our method on several time lapses of real outdoor scenes.