32,301 research outputs found
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
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
Sensor networks and distributed CSP: communication, computation and complexity
We introduce SensorDCSP, a naturally distributed benchmark based on a real-world application that arises in the context of networked distributed systems. In order to study the performance of Distributed CSP (DisCSP) algorithms in a truly distributed setting, we use a discrete-event network simulator, which allows us to model the impact of different network traffic conditions on the performance of the algorithms. We consider two complete DisCSP algorithms: asynchronous backtracking (ABT) and asynchronous weak commitment search (AWC), and perform performance comparison for these algorithms on both satisfiable and unsatisfiable instances of SensorDCSP. We found that random delays (due to network traffic or in some cases actively introduced by the agents) combined with a dynamic decentralized restart strategy can improve the performance of DisCSP algorithms. In addition, we introduce GSensorDCSP, a plain-embedded version of SensorDCSP that is closely related to various real-life dynamic tracking systems. We perform both analytical and empirical study of this benchmark domain. In particular, this benchmark allows us to study the attractiveness of solution repairing for solving a sequence of DisCSPs that represent the dynamic tracking of a set of moving objects.This work was supported in part by AFOSR (F49620-01-1-0076, Intelligent Information Systems Institute and MURI F49620-01-1-0361), CICYT (TIC2001-1577-C03-03 and TIC2003-00950), DARPA (F30602-00-2- 0530), an NSF CAREER award (IIS-9734128), and an Alfred P. Sloan Research Fellowship. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of the US Government
- …