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

Topological image modification for object detection and topological image processing of skin lesions

We propose a new method based on Topological Data Analysis (TDA) consisting of Topological Image Modification (TIM) and Topological Image Processing (TIP) for object detection. Through this newly introduced method, we artificially destruct irrelevant objects, and construct new objects with known topological properties in irrelevant regions of an image. This ensures that we are able to identify the important objects in relevant regions of the image. We do this by means of persistent homology, which allows us to simultaneously select appropriate thresholds, as well as the objects corresponding to these thresholds, and separate them from the noisy background of an image. This leads to a new image, processed in a completely unsupervised manner, from which one may more efficiently extract important objects. We demonstrate the usefulness of this proposed method for topological image processing through a case-study of unsupervised segmentation of the ISIC 2018 skin lesion images. Code for this project is available on https://bitbucket.org/ghentdatascience/topimgprocess

CG2Real: Improving the Realism of Computer Generated Images using a Large Collection of Photographs

Computer Graphics (CG) has achieved a high level of realism, producing strikingly vivid images. This realism, however, comes at the cost of long and often expensive manual modeling, and most often humans can still distinguish between CG images and real images. We present a novel method to make CG images look more realistic that is simple and accessible to novice users. Our system uses a large collection of photographs gathered from online repositories. Given a CG image, we retrieve a small number of real images with similar global structure. We identify corresponding regions between the CG and real images using a novel mean-shift cosegmentation algorithm. The user can then automatically transfer color, tone, and texture from matching regions to the CG image. Our system only uses image processing operations and does not require a 3D model of the scene, making it fast and easy to integrate into digital content creation workflows. Results of a user study show that our improved CG images appear more realistic than the originals

Combining Geometric and Topological Information for Boundary Estimation

A fundamental problem in computer vision is boundary estimation, where the goal is to delineate the boundary of objects in an image. In this paper, we propose a method which jointly incorporates geometric and topological information within an image to simultaneously estimate boundaries for objects within images with more complex topologies. We use a topological clustering-based method to assist initialization of the Bayesian active contour model. This combines pixel clustering, boundary smoothness, and potential prior shape information to produce an estimated object boundary. Active contour methods are knownto be extremely sensitive to algorithm initialization, relying on the user to provide a reasonable starting curve to the algorithm. In the presence of images featuring objects with complex topological structures, such as objects with holes or multiple objects, the user must initialize separate curves for each boundary of interest. Our proposed topologically-guided method can provide an interpretable, smart initialization in these settings, freeing up the user from potential pitfalls associated with objects of complex topological structure. We provide a detailed simulation study comparing our initialization to boundary estimates obtained from standard segmentation algorithms. The method is demonstrated on artificial image datasets from computer vision, as well as real-world applications to skin lesion and neural cellular images, for which multiple topological features can be identified.Comment: 38 pages with appendices, 15 figure

Finding semantic structures in image hierarchies using Laplacian graph energy

Many segmentation algorithms describe images in terms of a hierarchy of regions. Although such hierarchies can produce state of the art segmentations and have many applications, they often contain more data than is required for an efficient description. This paper shows Laplacian graph energy is a generic measure that can be used to identify semantic structures within hierarchies, independently of the algorithm that produces them. Quantitative experimental validation using hierarchies from two state of art algorithms show we can reduce the number of levels and regions in a hierarchy by an order of magnitude with little or no loss in performance when compared against human produced ground truth. We provide a tracking application that illustrates the value of reduced hierarchies

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions

Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single regions or small groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps.National Institutes of Health (U.S.) (Grant PN2EY016525)National Institutes of Health (U.S.) (Grant R01GM079429)National Institutes of Health (U.S.) (Grant P41RR02250)National Science Foundation (U.S.) (IIS-0705644

An intuitive model of perceptual grouping for HCI design

ABSTRACT Understanding and exploiting the abilities of the human visual system is an important part of the design of usable user interfaces and information visualizations. Good design enables quick, easy and veridical perception of key components of that design. An important facet of human vision is its ability to seemingly effortlessly perform "perceptual organization"; it transforms individual feature estimates into perception of coherent regions, structures, and objects. We perceive regions grouped by proximity and feature similarity, grouping of curves by good continuation, and grouping of regions of coherent texture. In this paper, we discuss a simple model for a broad range of perceptual grouping phenomena. It takes as input an arbitrary image, and returns a structure describing the predicted visual organization of the image. We demonstrate that this model can capture aspects of traditional design rules, and predicts visual percepts in classic perceptual grouping displays