The watershed transform: definitions, algorithms and parallelization strategies
TL;DR: A critical review of several definitions of watershed transform and associated sequential algorithms is presented in this paper, where the need to distinguish between definition, algorithm specification and algorithm implementation is pointed out.
Abstract: The watershed transform is the method of choice for image segmentation in the field of mathematical morphology. We present a critical review of several definitions of the watershed transform and the associated sequential algorithms, and discuss various issues which often cause confusion in the literature. The need to distinguish between definition, algorithm specification and algorithm implementation is pointed out. Various examples are given which illustrate differences between watershed transforms based on different definitions and/or implementations. The second part of the paper surveys approaches for parallel implementation of sequential watershed algorithms.
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TL;DR: A novel toolbox for subcellular colocalization analysis under ImageJ is created that integrates current global statistic methods and a novel object‐based approach to assess proteins residing on intracellular structures by fluorescence microscopy.
Abstract: Summary It is generally accepted that the functional compartmentalization of eukaryotic cells is reflected by the differential occurrence of proteins in their compartments. The location and physiological function of a protein are closely related; local information of a protein is thus crucial to understanding its role in biological processes. The visualization of proteins residing on intracellular structures by fluorescence microscopy has become a routine approach in cell biology and is increasingly used to assess their colocalization with well-characterized markers. However, imageanalysis methods for colocalization studies are a field of contention and enigma. We have therefore undertaken to review the most currently used colocalization analysis methods, introducing the basic optical concepts important for image acquisition and subsequent analysis. We provide a summary of practical tips for image acquisition and treatment that should precede proper colocalization analysis. Furthermore, we discuss the application and feasibility of colocalization tools for various biological colocalization situations and discuss their respective strengths and weaknesses. We have created a novel toolbox for subcellular colocalization analysis under Image J, named JACoP, that integrates current global statistic methods and a novel object-based approach.
4,195 citations
TL;DR: An improvement to the watershed transform is presented that enables the introduction of prior information in its calculation, and a method to combine the watershedtransform and atlas registration, through the use of markers is introduced.
Abstract: The watershed transform has interesting properties that make it useful for many different image segmentation applications: it is simple and intuitive, can be parallelized, and always produces a complete division of the image. However, when applied to medical image analysis, it has important drawbacks (oversegmentation, sensitivity to noise, poor detection of thin or low signal to noise ratio structures). We present an improvement to the watershed transform that enables the introduction of prior information in its calculation. We propose to introduce this information via the use of a previous probability calculation. Furthermore, we introduce a method to combine the watershed transform and atlas registration, through the use of markers. We have applied our new algorithm to two challenging applications: knee cartilage and gray matter/white matter segmentation in MR images. Numerical validation of the results is provided, demonstrating the strength of the algorithm for medical image segmentation.
769 citations
01 Oct 2017
TL;DR: In this article, a structured segment network (SSN) is proposed to model the temporal structure of each action instance via a structured temporal pyramid, and a decomposed discriminative model comprising two classifiers, respectively for classifying actions and determining completeness.
Abstract: Detecting actions in untrimmed videos is an important yet challenging task. In this paper, we present the structured segment network (SSN), a novel framework which models the temporal structure of each action instance via a structured temporal pyramid. On top of the pyramid, we further introduce a decomposed discriminative model comprising two classifiers, respectively for classifying actions and determining completeness. This allows the framework to effectively distinguish positive proposals from background or incomplete ones, thus leading to both accurate recognition and localization. These components are integrated into a unified network that can be efficiently trained in an end-to-end fashion. Additionally, a simple yet effective temporal action proposal scheme, dubbed temporal actionness grouping (TAG) is devised to generate high quality action proposals. On two challenging benchmarks, THUMOS14 and ActivityNet, our method remarkably outperforms previous state-of-the-art methods, demonstrating superior accuracy and strong adaptivity in handling actions with various temporal structures.
578 citations
TL;DR: This study presents, discusses, and extracts the major trends from an exhaustive overview of various nuclei detection, segmentation, feature computation, and classification techniques used in histopathology imagery, specifically in hematoxylin-eosin and immunohistochemical staining protocols.
Abstract: Digital pathology represents one of the major evolutions in modern medicine. Pathological examinations constitute the gold standard in many medical protocols, and also play a critical and legal role in the diagnosis process. In the conventional cancer diagnosis, pathologists analyze biopsies to make diagnostic and prognostic assessments, mainly based on the cell morphology and architecture distribution. Recently, computerized methods have been rapidly evolving in the area of digital pathology, with growing applications related to nuclei detection, segmentation, and classification. In cancer research, these approaches have played, and will continue to play a key (often bottleneck) role in minimizing human intervention, consolidating pertinent second opinions, and providing traceable clinical information. Pathological studies have been conducted for numerous cancer detection and grading applications, including brain, breast, cervix, lung, and prostate cancer grading. Our study presents, discusses, and extracts the major trends from an exhaustive overview of various nuclei detection, segmentation, feature computation, and classification techniques used in histopathology imagery, specifically in hematoxylin-eosin and immunohistochemical staining protocols. This study also enables us to measure the challenges that remain, in order to reach robust analysis of whole slide images, essential high content imaging with diagnostic biomarkers and prognosis support in digital pathology.
567 citations
TL;DR: A precise definition of the image foresting transform is given, and a procedure to compute it-a generalization of Dijkstra's algorithm-with a proof of correctness is given.
Abstract: The image foresting transform (IFT) is a graph-based approach to the design of image processing operators based on connectivity. It naturally leads to correct and efficient implementations and to a better understanding of how different operators relate to each other. We give here a precise definition of the IFT, and a procedure to compute it-a generalization of Dijkstra's algorithm-with a proof of correctness. We also discuss implementation issues and illustrate the use of the IFT in a few applications.
549 citations
References
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TL;DR: A tree is a graph with one and only one path between every two nodes, where at least one path exists between any two nodes and the length of each branch is given.
Abstract: We consider n points (nodes), some or all pairs of which are connected by a branch; the length of each branch is given. We restrict ourselves to the case where at least one path exists between any two nodes. We now consider two problems. Problem 1. Constrnct the tree of minimum total length between the n nodes. (A tree is a graph with one and only one path between every two nodes.) In the course of the construction that we present here, the branches are subdivided into three sets: I. the branches definitely assignec~ to the tree under construction (they will form a subtree) ; II. the branches from which the next branch to be added to set I, will be selected ; III. the remaining branches (rejected or not yet considered). The nodes are subdivided into two sets: A. the nodes connected by the branches of set I, B. the remaining nodes (one and only one branch of set II will lead to each of these nodes), We start the construction by choosing an arbitrary node as the only member of set A, and by placing all branches that end in this node in set II. To start with, set I is empty. From then onwards we perform the following two steps repeatedly. Step 1. The shortest branch of set II is removed from this set and added to
22,704 citations
Book•
01 Jan 1990TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
Abstract: From the Publisher:
The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures. Like the first edition,this text can also be used for self-study by technical professionals since it discusses engineering issues in algorithm design as well as the mathematical aspects.
In its new edition,Introduction to Algorithms continues to provide a comprehensive introduction to the modern study of algorithms. The revision has been updated to reflect changes in the years since the book's original publication. New chapters on the role of algorithms in computing and on probabilistic analysis and randomized algorithms have been included. Sections throughout the book have been rewritten for increased clarity,and material has been added wherever a fuller explanation has seemed useful or new information warrants expanded coverage.
As in the classic first edition,this new edition of Introduction to Algorithms presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers. Further,the algorithms are presented in pseudocode to make the book easily accessible to students from all programming language backgrounds.
Each chapter presents an algorithm,a design technique,an application area,or a related topic. The chapters are not dependent on one another,so the instructor can organize his or her use of the book in the way that best suits the course's needs. Additionally,the new edition offers a 25% increase over the first edition in the number of problems,giving the book 155 problems and over 900 exercises thatreinforcethe concepts the students are learning.
21,651 citations
Book•
11 Feb 1984
TL;DR: This invaluable reference helps readers assess and simplify problems and their essential requirements and complexities, giving them all the necessary data and methodology to master current theoretical developments and applications, as well as create new ones.
Abstract: Image Processing and Mathematical Morphology-Frank Y. Shih 2009-03-23 In the development of digital multimedia, the importance and impact of image processing and mathematical morphology are well documented in areas ranging from automated vision detection and inspection to object recognition, image analysis and pattern recognition. Those working in these ever-evolving fields require a solid grasp of basic fundamentals, theory, and related applications—and few books can provide the unique tools for learning contained in this text. Image Processing and Mathematical Morphology: Fundamentals and Applications is a comprehensive, wide-ranging overview of morphological mechanisms and techniques and their relation to image processing. More than merely a tutorial on vital technical information, the book places this knowledge into a theoretical framework. This helps readers analyze key principles and architectures and then use the author’s novel ideas on implementation of advanced algorithms to formulate a practical and detailed plan to develop and foster their own ideas. The book: Presents the history and state-of-the-art techniques related to image morphological processing, with numerous practical examples Gives readers a clear tutorial on complex technology and other tools that rely on their intuition for a clear understanding of the subject Includes an updated bibliography and useful graphs and illustrations Examines several new algorithms in great detail so that readers can adapt them to derive their own solution approaches This invaluable reference helps readers assess and simplify problems and their essential requirements and complexities, giving them all the necessary data and methodology to master current theoretical developments and applications, as well as create new ones.
9,566 citations
TL;DR: A fast and flexible algorithm for computing watersheds in digital gray-scale images is introduced, based on an immersion process analogy, which is reported to be faster than any other watershed algorithm.
Abstract: A fast and flexible algorithm for computing watersheds in digital gray-scale images is introduced. A review of watersheds and related motion is first presented, and the major methods to determine watersheds are discussed. The algorithm is based on an immersion process analogy, in which the flooding of the water in the picture is efficiently simulated using of queue of pixel. It is described in detail provided in a pseudo C language. The accuracy of this algorithm is proven to be superior to that of the existing implementations, and it is shown that its adaptation to any kind of digital grid and its generalization to n-dimensional images (and even to graphs) are straightforward. The algorithm is reported to be faster than any other watershed algorithm. Applications of this algorithm with regard to picture segmentation are presented for magnetic resonance (MR) imagery and for digital elevation models. An example of 3-D watershed is also provided. >
4,983 citations
Book•
01 Jan 1994TL;DR: Using MPI as mentioned in this paper provides a thoroughly updated guide to the MPI (Message-Passing Interface) standard library for writing programs for parallel computers, including a comparison of MPI with sockets.
Abstract: This book offers a thoroughly updated guide to the MPI (Message-Passing Interface) standard library for writing programs for parallel computers Since the publication of the previous edition of Using MPI, parallel computing has become mainstream Today, applications run on computers with millions of processors; multiple processors sharing memory and multicore processors with multiple hardware threads per core are common The MPI-3 Forum recently brought the MPI standard up to date with respect to developments in hardware capabilities, core language evolution, the needs of applications, and experience gained over the years by vendors, implementers, and users This third edition of Using MPI reflects these changes in both text and example code The book takes an informal, tutorial approach, introducing each concept through easy-to-understand examples, including actual code in C and Fortran Topics include using MPI in simple programs, virtual topologies, MPI datatypes, parallel libraries, and a comparison of MPI with sockets For the third edition, example code has been brought up to date; applications have been updated; and references reflect the recent attention MPI has received in the literature A companion volume, Using Advanced MPI, covers more advanced topics, including hybrid programming and coping with large data
2,666 citations