Template-Cut: A Pattern-Based Segmentation Paradigm

We present a scale-invariant, template-based segmentation paradigm that sets up a graph and performs a graph cut to separate an object from the background. Typically graph-based schemes distribute the nodes of the graph uniformly and equidistantly on the image, and use a regularizer to bias the cut towards a particular shape. The strategy of uniform and equidistant nodes does not allow the cut to prefer more complex structures, especially when areas of the object are indistinguishable from the background. We propose a solution by introducing the concept of a "template shape" of the target object in which the nodes are sampled non-uniformly and non-equidistantly on the image. We evaluate it on 2D-images where the object's textures and backgrounds are similar, and large areas of the object have the same gray level appearance as the background. We also evaluate it in 3D on 60 brain tumor datasets for neurosurgical planning purposes.Comment: 8 pages, 6 figures, 3 tables, 6 equations, 51 reference

Cube-Cut: Vertebral Body Segmentation in MRI-Data through Cubic-Shaped Divergences

In this article, we present a graph-based method using a cubic template for volumetric segmentation of vertebrae in magnetic resonance imaging (MRI) acquisitions. The user can define the degree of deviation from a regular cube via a smoothness value Delta. The Cube-Cut algorithm generates a directed graph with two terminal nodes (s-t-network), where the nodes of the graph correspond to a cubic-shaped subset of the image's voxels. The weightings of the graph's terminal edges, which connect every node with a virtual source s or a virtual sink t, represent the affinity of a voxel to the vertebra (source) and to the background (sink). Furthermore, a set of infinite weighted and non-terminal edges implements the smoothness term. After graph construction, a minimal s-t-cut is calculated within polynomial computation time, which splits the nodes into two disjoint units. Subsequently, the segmentation result is determined out of the source-set. A quantitative evaluation of a C++ implementation of the algorithm resulted in an average Dice Similarity Coefficient (DSC) of 81.33% and a running time of less than a minute.Comment: 23 figures, 2 tables, 43 references, PLoS ONE 9(4): e9338

Advancing Operating Systems via Aspect-Oriented Programming

Operating system kernels are among the most complex pieces of software in existence to- day. Maintaining the kernel code and developing new functionality is increasingly compli- cated, since the amount of required features has risen significantly, leading to side ef fects that can be introduced inadvertedly by changing a piece of code that belongs to a completely dif ferent context. Software developers try to modularize their code base into separate functional units. Some of the functionality or “concerns” required in a kernel, however, does not fit into the given modularization structure; this code may then be spread over the code base and its implementation tangled with code implementing dif ferent concerns. These so-called “crosscutting concerns” are especially dif ficult to handle since a change in a crosscutting concern implies that all relevant locations spread throughout the code base have to be modified. Aspect-Oriented Software Development (AOSD) is an approach to handle crosscutting concerns by factoring them out into separate modules. The “advice” code contained in these modules is woven into the original code base according to a pointcut description, a set of interaction points (joinpoints) with the code base. To be used in operating systems, AOSD requires tool support for the prevalent procedu- ral programming style as well as support for weaving aspects. Many interactions in kernel code are dynamic, so in order to implement non-static behavior and improve performance, a dynamic weaver that deploys and undeploys aspects at system runtime is required. This thesis presents an extension of the “C” programming language to support AOSD. Based on this, two dynamic weaving toolkits – TOSKANA and TOSKANA-VM – are presented to permit dynamic aspect weaving in the monolithic NetBSD kernel as well as in a virtual- machine and microkernel-based Linux kernel running on top of L4. Based on TOSKANA, applications for this dynamic aspect technology are discussed and evaluated. The thesis closes with a view on an aspect-oriented kernel structure that maintains coherency and handles crosscutting concerns using dynamic aspects while enhancing de- velopment methods through the use of domain-specific programming languages

Using a LowLevel Virtual Machine to improve dynamic aspect support in operating system kernels

ABSTRACT Current implementations of software providing dynamic aspect functionality in operating system (OS) kernels are quite restricted in the possible joinpoint types for native code they are able to support. Most of the projects implementing advice for native code use basic technologies adopted from instrumentation methods which allow to provide before, after and around joinpoints for functions. More elaborate joinpoints, however, are not available since support for monitoring native code execution in current CPUs is very restricted without extensive extensions of the compiler toolchain. To realize improved ways of aspect activation in OS kernels, we present an architecture that provides an efficient low-level virtual machine running on top of a microkernel system in cooperation with an aspect deployment service to provide novel ways of aspect activation in kernel environments

Fault-tolerant Distributed Reactive Programming

In this paper, we present a holistic approach to provide fault tolerance for distributed reactive programming. Our solution automatically stores and recovers program state to handle crashes, automatically updates and shares distributed parts of the state to provide eventual consistency, and handles errors in a fine-grained manner to allow precise manual control when necessary. By making use of the reactive programming paradigm, we provide these mechanisms without changing the behavior of existing programs and with reasonable performance, as indicated by our experimental evaluation