The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd

Video modeling via implicit motion representations

Video modeling refers to the development of analytical representations for explaining the intensity distribution in video signals. Based on the analytical representation, we can develop algorithms for accomplishing particular video-related tasks. Therefore video modeling provides us a foundation to bridge video data and related-tasks. Although there are many video models proposed in the past decades, the rise of new applications calls for more efficient and accurate video modeling approaches.;Most existing video modeling approaches are based on explicit motion representations, where motion information is explicitly expressed by correspondence-based representations (i.e., motion velocity or displacement). Although it is conceptually simple, the limitations of those representations and the suboptimum of motion estimation techniques can degrade such video modeling approaches, especially for handling complex motion or non-ideal observation video data. In this thesis, we propose to investigate video modeling without explicit motion representation. Motion information is implicitly embedded into the spatio-temporal dependency among pixels or patches instead of being explicitly described by motion vectors.;Firstly, we propose a parametric model based on a spatio-temporal adaptive localized learning (STALL). We formulate video modeling as a linear regression problem, in which motion information is embedded within the regression coefficients. The coefficients are adaptively learned within a local space-time window based on LMMSE criterion. Incorporating a spatio-temporal resampling and a Bayesian fusion scheme, we can enhance the modeling capability of STALL on more general videos. Under the framework of STALL, we can develop video processing algorithms for a variety of applications by adjusting model parameters (i.e., the size and topology of model support and training window). We apply STALL on three video processing problems. The simulation results show that motion information can be efficiently exploited by our implicit motion representation and the resampling and fusion do help to enhance the modeling capability of STALL.;Secondly, we propose a nonparametric video modeling approach, which is not dependent on explicit motion estimation. Assuming the video sequence is composed of many overlapping space-time patches, we propose to embed motion-related information into the relationships among video patches and develop a generic sparsity-based prior for typical video sequences. First, we extend block matching to more general kNN-based patch clustering, which provides an implicit and distributed representation for motion information. We propose to enforce the sparsity constraint on a higher-dimensional data array signal, which is generated by packing the patches in the similar patch set. Then we solve the inference problem by updating the kNN array and the wanted signal iteratively. Finally, we present a Bayesian fusion approach to fuse multiple-hypothesis inferences. Simulation results in video error concealment, denoising, and deartifacting are reported to demonstrate its modeling capability.;Finally, we summarize the proposed two video modeling approaches. We also point out the perspectives of implicit motion representations in applications ranging from low to high level problems

Accurate automatic object 4D tracking in digital in‑line holographic microscopy based on computationally rendered dark fields

Building on Gabor seminal principle, digital in-line holographic microscopy provides efficient means for space-time investigations of large volumes of interest. Thus, it has a pivotal impact on particle tracking that is crucial in advancing various branches of science and technology, e.g., microfluidics and biophysical processes examination (cell motility, migration, interplay etc.). Well-established algorithms often rely on heavily regularized inverse problem modelling and encounter limitations in terms of tracking accuracy, hologram signal-to-noise ratio, accessible object volume, particle concentration and computational burden. This work demonstrates the DarkTrack algorithm a new approach to versatile, fast, precise, and robust 4D holographic tracking based on deterministic computationally rendered high-contrast dark fields. Its unique capabilities are quantitatively corroborated employing a novel numerical engine for simulating Gabor holographic recording of time-variant volumes filled with predefined dynamic particles. Our solution accounts for multiple scattering and thus it is poised to secure an important gap in holographic particle tracking technology and allow for ground-truth-driven benchmarking and quantitative assessment of tracking algorithms. Proof-of-concept experimental evaluation of DarkTrack is presented via analyzing live spermatozoa. Software supporting both novel numerical holographic engine and DarkTrack algorithm is made open access, which opens new possibilities and sets the stage for democratization of robust holographic 4D particle examination

Contour extraction from HVEM image of microvessel using active contour models

This thesis reports the research results on automatic contour extraction from high voltage electron microscope (HVEM) image of thick cross section montages of small blood vessels. The previous work on this subject, which was based on the conventional edge detection operations combined with edge linking, has proven inadequate to describe the inner structural compartments of microvessels. In this thesis, an active contour model (commonly referred to as Snakes ) has been applied to advance the previous work. Active contour models have proven themselves to be a powerful and flexible paradigm for many problems in image understanding, especially in contour extraction from medical images. With the developed energy functions, the active contour is attracted towards the edges under the action of internal forces (describing some elasticity properties of the contour), image forces and external forces by means of minimization of the energy functions. Based on this active model, an effective algorithm is implemented as a powerful tool for 2-D contour extraction in our problem for the first time. The results thus obtained turn out to be encouraging

Image morphological processing

Mathematical Morphology with applications in image processing and analysis has been becoming increasingly important in today\u27s technology. Mathematical Morphological operations, which are based on set theory, can extract object features by suitably shaped structuring elements. Mathematical Morphological filters are combinations of morphological operations that transform an image into a quantitative description of its geometrical structure based on structuring elements. Important applications of morphological operations are shape description, shape recognition, nonlinear filtering, industrial parts inspection, and medical image processing. In this dissertation, basic morphological operations, properties and fuzzy morphology are reviewed. Existing techniques for solving corner and edge detection are presented. A new approach to solve corner detection using regulated mathematical morphology is presented and is shown that it is more efficient in binary images than the existing mathematical morphology based asymmetric closing for corner detection. A new class of morphological operations called sweep mathematical morphological operations is developed. The theoretical framework for representation, computation and analysis of sweep morphology is presented. The basic sweep morphological operations, sweep dilation and sweep erosion, are defined and their properties are studied. It is shown that considering only the boundaries and performing operations on the boundaries can substantially reduce the computation. Various applications of this new class of morphological operations are discussed, including the blending of swept surfaces with deformations, image enhancement, edge linking and shortest path planning for rotating objects. Sweep mathematical morphology is an efficient tool for geometric modeling and representation. The sweep dilation/erosion provides a natural representation of sweep motion in the manufacturing processes. A set of grammatical rules that govern the generation of objects belonging to the same group are defined. Earley\u27s parser serves in the screening process to determine whether a pattern is a part of the language. Finally, summary and future research of this dissertation are provided