A quasi-linear algorithm to compute the tree of shapes of n-D images

International audienceTo compute the morphological self-dual representation of images, namely the tree of shapes, the state-of-the-art algorithms do not have a satisfactory time complexity. Furthermore the proposed algorithms are only effective for 2D images and they are far from being simple to implement. That is really penalizing since a self-dual representation of images is a structure that gives rise to many powerful operators and applications, and that could be very useful for 3D images. In this paper we propose a simple-to-write algorithm to compute the tree of shapes; it works for \nD images and has a quasi-linear complexity when data quantization is low, typically 12~bits or less. To get that result, this paper introduces a novel representation of images that has some amazing properties of continuity, while remaining discrete

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research

Remote Sensing Image Classification Using Attribute Filters Defined over the Tree of Shapes

International audience—Remotely sensed images with very high spatial resolution provide a detailed representation of the surveyed scene with a geometrical resolution that at the present can be up to 30 cm (WorldView-3). A set of powerful image processing operators have been defined in the mathematical morphology framework. Among those, connected operators (e.g., attribute filters) have proven their effectiveness in processing very high resolution images. Attribute filters are based on attributes which can be efficiently implemented on tree-based image representations. In this work, we considered the definition of min, max, direct and subtractive filter rules for the computation of attribute filters over the tree of shapes representation. We study their performance on the classification of remotely sensed images. We compare the classification results over the tree of shapes with the results obtained when the same rules are applied on the component trees. The random forest is used as a baseline classifier and the experiments are conducted using multispectral data sets acquired by QuickBird and IKONOS sensors over urban areas

On making nD images well-composed by a self-dual local interpolation

International audienceNatural and synthetic discrete images are generally not well-composed, leading to many topological issues: connectivities in binary images are not equivalent, the Jordan Separation theorem is not true anymore, and so on. Conversely, making images well-composed solves those problems and then gives access to many powerful tools already known in mathematical morphology as the Tree of Shapes which is of our principal interest. In this paper, we present two main results: a characterization of 3D well-composed gray-valued images; and a counter-example showing that no local self-dual interpolation satisfying a classical set of properties makes well-composed images with one subdivision in 3D, as soon as we choose the mean operator to interpolate in 1D. Then, we briefly discuss various constraints that could be interesting to change to make the problem solvable in nD

Distributed Component Forests in 2-D:Hierarchical Image Representations Suitable for Tera-Scale Images

The standard representations known as component trees, used in morphological connected attribute filtering and multi-scale analysis, are unsuitable for cases in which either the image itself or the tree do not fit in the memory of a single compute node. Recently, a new structure has been developed which consists of a collection of modified component trees, one for each image tile. It has to-date only been applied to fairly simple image filtering based on area. In this paper, we explore other applications of these distributed component forests, in particular to multi-scale analysis such as pattern spectra, and morphological attribute profiles and multi-scale leveling segmentations

A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes

Electron Cryo-Microscopy or cryo-EM is an area that has received much attention in the recent past. Compared to the traditional methods of X-Ray Crystallography and NMR Spectroscopy, cryo-EM can be used to image much larger complexes, in many different conformations, and under a wide range of biochemical conditions. This is because it does not require the complex to be crystallisable. However, cryo-EM reconstructions are limited to intermediate resolutions, with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure identification. In this dissertation, we present a suite of geometric algorithms to address several aspects of protein modeling using cryo-EM density maps. Specifically, we develop novel methods to capture the shape of density volumes as geometric skeletons. We then use these skeletons to find secondary structure elements: SSEs) of a given protein, to identify the correspondence between these SSEs and those predicted from the primary sequence, and to register high-resolution protein structures onto the density volume. In addition, we designed and developed Gorgon, an interactive molecular modeling system, that integrates the above methods with other interactive routines to generate reliable and accurate protein backbone models