Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines

Many automatically analyzable scientific questions are well-posed and offer a variety of information about the expected outcome a priori. Although often being neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and the direct information about the ambiguity inherent in the extracted data. We present a new concept for the estimation and propagation of uncertainty involved in image analysis operators. This allows using simple processing operators that are suitable for analyzing large-scale 3D+t microscopy images without compromising the result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it enhance the result quality of various processing operators. All presented concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. Furthermore, the functionality of the proposed approach is validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. Especially, the automated analysis of terabyte-scale microscopy data will benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. The generality of the concept, however, makes it also applicable to practically any other field with processing strategies that are arranged as linear pipelines.Comment: 39 pages, 12 figure

EmbedTrack—Simultaneous Cell Segmentation and Tracking Through Learning Offsets and Clustering Bandwidths

A systematic analysis of the cell behavior requires automated approaches for cell segmentation and tracking. While deep learning has been successfully applied for the task of cell segmentation, there are few approaches for simultaneous cell segmentation and tracking using deep learning. Here, we present EmbedTrack, a single convolutional neural network for simultaneous cell segmentation and tracking which predicts easy to interpret embeddings. As embeddings, offsets of cell pixels to their cell center and bandwidths are learned. We benchmark our approach on nine 2D data sets from the Cell Tracking Challenge, where our approach performs on seven out of nine data sets within the top 3 contestants including three top 1 performances. The source code is publicly available at https://git.scc.kit.edu/kit-loe-ge/embedtrack.Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessibl

Cell Segmentation and Tracking using CNN-Based Distance Predictions and a Graph-Based Matching Strategy

The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching cells in images with a low signal-to-noise-ratio is still a challenging problem. In this paper, we present a method for the segmentation of touching cells in microscopy images. By using a novel representation of cell borders, inspired by distance maps, our method is capable to utilize not only touching cells but also close cells in the training process. Furthermore, this representation is notably robust to annotation errors and shows promising results for the segmentation of microscopy images containing in the training data underrepresented or not included cell types. For the prediction of the proposed neighbor distances, an adapted U-Net convolutional neural network (CNN) with two decoder paths is used. In addition, we adapt a graph-based cell tracking algorithm to evaluate our proposed method on the task of cell tracking. The adapted tracking algorithm includes a movement estimation in the cost function to re-link tracks with missing segmentation masks over a short sequence of frames. Our combined tracking by detection method has proven its potential in the IEEE ISBI 2020 Cell Tracking Challenge (http://celltrackingchallenge.net/) where we achieved as team KIT-Sch-GE multiple top three rankings including two top performances using a single segmentation model for the diverse data sets.Comment: 25 pages, 14 figures, methods of the team KIT-Sch-GE for the IEEE ISBI 2020 Cell Tracking Challeng

Context-Aware Composition of Agent Policies by Markov Decision Process Entity Embeddings and Agent Ensembles

Computational agents support humans in many areas of life and are therefore found in heterogeneous contexts. This means they operate in rapidly changing environments and can be confronted with huge state and action spaces. In order to perform services and carry out activities in a goal-oriented manner, agents require prior knowledge and therefore have to develop and pursue context-dependent policies. However, prescribing policies in advance is limited and inflexible, especially in dynamically changing environments. Moreover, the context of an agent determines its choice of actions. Since the environments can be stochastic and complex in terms of the number of states and feasible actions, activities are usually modelled in a simplified way by Markov decision processes so that, e.g., agents with reinforcement learning are able to learn policies, that help to capture the context and act accordingly to optimally perform activities. However, training policies for all possible contexts using reinforcement learning is time-consuming. A requirement and challenge for agents is to learn strategies quickly and respond immediately in cross-context environments and applications, e.g., the Internet, service robotics, cyber-physical systems. In this work, we propose a novel simulation-based approach that enables a) the representation of heterogeneous contexts through knowledge graphs and entity embeddings and b) the context-aware composition of policies on demand by ensembles of agents running in parallel. The evaluation we conducted with the "Virtual Home" dataset indicates that agents with a need to switch seamlessly between different contexts, can request on-demand composed policies that lead to the successful completion of context-appropriate activities without having to learn these policies in lengthy training steps and episodes, in contrast to agents that use reinforcement learning.Comment: 30 pages, 11 figures, 9 tables, 3 listings, Re-submitted to Semantic Web Journal, Currently, under revie

Simulation of Synthetically Degraded Tracking Data to Benchmark MOT Metrics

Multiple object tracking (MOT) is an essential task in computer vision, with many practical applications in surveillance, robotics, autonomous driving, and biology. To compare different MOT algorithms efficiently and select the best MOT algorithm for an application, we rely on tracking metrics that reduce the performance of a tracking algorithm to a single score. However, there is a lack in testing the tracking metrics themselves, which can result in unnoticed biases or flaws in tracking metrics that can influence the decision of selecting the best tracking algorithm. To check tracking metrics for possible limitations or biases towards penalizing specific tracking errors, a standardized evaluation of tracking metrics is needed. We propose benchmarking tracking metrics using synthetic, erroneous tracking results that simulate real-world tracking errors. First, we select common real-world tracking errors from the literature and describe how to emulate them. Then, we validate our approach by reproducing previously found tracking metric limitations through simulating specific tracking errors. In addition, our benchmark reveals a before unreported limitation in the tracking metric AOGM. Moreover, we make an implementation of our benchmark publicly available

Proceedings. 26. Workshop Computational Intelligence, Dortmund, 24. - 25. November 2016

Dieser Tagungsband enthält die Beiträge des 26. Workshops Computational Intelligence. Die Schwerpunkte sind Methoden, Anwendungen und Tools für Fuzzy-Systeme, Künstliche Neuronale Netze, Evolutionäre Algorithmen und Data-Mining-Verfahren sowie der Methodenvergleich anhand von industriellen und Benchmark-Problemen

Design of Transformation Initiatives Implementing Organisational Agility -- An Empirical Study

This study uses 125 responses from companies of all sizes headquartered in Germany, Switzerland, France and UK to reveal perceptions of the drivers of organisational agility. It further investigates current understanding of managing principles of multiple organisational dimensions such as culture, values, leadership, organisational structure, processes and others to achieve greater organisational agility. The data set is disaggregated into four major profiles of agile organisations: laggards, execution specialists, experimenters, and leaders. The approach to agile transformation is analysed by each of those profiles. While the positive effect from a more holistic approach is confirmed, leaders tend to focus more on processes and products rather than project work. Respondents perceive that IT, product development and research are most agile functions within their organisations, while human resources, finance and administration are considered being not agile. Further, organisations with higher levels of organisational agility tend use more than one agile scaling framework. Implications on theories of agile transformations and organisational design are discussed