NEFI: Network Extraction From Images

Networks and network-like structures are amongst the central building blocks of many technological and biological systems. Given a mathematical graph representation of a network, methods from graph theory enable a precise investigation of its properties. Software for the analysis of graphs is widely available and has been applied to graphs describing large scale networks such as social networks, protein-interaction networks, etc. In these applications, graph acquisition, i.e., the extraction of a mathematical graph from a network, is relatively simple. However, for many network-like structures, e.g. leaf venations, slime molds and mud cracks, data collection relies on images where graph extraction requires domain-specific solutions or even manual. Here we introduce Network Extraction From Images, NEFI, a software tool that automatically extracts accurate graphs from images of a wide range of networks originating in various domains. While there is previous work on graph extraction from images, theoretical results are fully accessible only to an expert audience and ready-to-use implementations for non-experts are rarely available or insufficiently documented. NEFI provides a novel platform allowing practitioners from many disciplines to easily extract graph representations from images by supplying flexible tools from image processing, computer vision and graph theory bundled in a convenient package. Thus, NEFI constitutes a scalable alternative to tedious and error-prone manual graph extraction and special purpose tools. We anticipate NEFI to enable the collection of larger datasets by reducing the time spent on graph extraction. The analysis of these new datasets may open up the possibility to gain new insights into the structure and function of various types of networks. NEFI is open source and available http://nefi.mpi-inf.mpg.de

Randomized algorithms for statistical image analysis and site percolation on square lattices

We propose a novel probabilistic method for detection of objects in noisy images. The method uses results from percolation and random graph theories. We present an algorithm that allows to detect objects of unknown shapes in the presence of random noise. The algorithm has linear complexity and exponential accuracy and is appropriate for real-time systems. We prove results on consistency and algorithmic complexity of our procedure.Comment: Submitted for publication on December 11, 200

Robust nonparametric detection of objects in noisy images

We propose a novel statistical hypothesis testing method for detection of objects in noisy images. The method uses results from percolation theory and random graph theory. We present an algorithm that allows to detect objects of unknown shapes in the presence of nonparametric noise of unknown level and of unknown distribution. No boundary shape constraints are imposed on the object, only a weak bulk condition for the object's interior is required. The algorithm has linear complexity and exponential accuracy and is appropriate for real-time systems. In this paper, we develop further the mathematical formalism of our method and explore important connections to the mathematical theory of percolation and statistical physics. We prove results on consistency and algorithmic complexity of our testing procedure. In addition, we address not only an asymptotic behavior of the method, but also a finite sample performance of our test.Comment: This paper initially appeared in 2010 as EURANDOM Report 2010-049. Link to the abstract at EURANDOM repository: http://www.eurandom.tue.nl/reports/2010/049-abstract.pdf Link to the paper at EURANDOM repository: http://www.eurandom.tue.nl/reports/2010/049-report.pd

Stochastic extraction of elongated curvilinear structures with applications

The automatic extraction of elongated curvilinear structures (CLSs) is an important task in various image processing applications, including numerous remote sensing, and biometrical and medical problems. To address this task, we develop a stochastic approach that relies on a fixed-grid, localized Radon transform for line segment extraction and a conditional random field model to incorporate local interactions and refine the extracted CLSs. We propose several different energy data terms, the appropriate choice of which allows us to process images with different noise and geometry properties. The contribution of this paper is the design of a flexible and robust elongated CLS extraction framework that is comparatively fast due to the use of a fixed-grid configuration and fast deterministic Radon-based line detector. We present several different applications of the developed approach, namely: 1) CLS extraction in mammographic images; 2) road networks extraction from optical remotely sensed images; and 3) line extraction from palmprint images. The experimental results demonstrate that the method is fairly robust to CLS curvature and can accurately extract blurred and low-contrast elongated CLS

Multiple testing, uncertainty and realistic pictures

We study statistical detection of grayscale objects in noisy images. The object of interest is of unknown shape and has an unknown intensity, that can be varying over the object and can be negative. No boundary shape constraints are imposed on the object, only a weak bulk condition for the object's interior is required. We propose an algorithm that can be used to detect grayscale objects of unknown shapes in the presence of nonparametric noise of unknown level. Our algorithm is based on a nonparametric multiple testing procedure. We establish the limit of applicability of our method via an explicit, closed-form, non-asymptotic and nonparametric consistency bound. This bound is valid for a wide class of nonparametric noise distributions. We achieve this by proving an uncertainty principle for percolation on finite lattices.Comment: This paper initially appeared in January 2011 as EURANDOM Report 2011-004. Link to the abstract at EURANDOM Repository: http://www.eurandom.tue.nl/reports/2011/004-abstract.pdf Link to the paper at EURANDOM Repository: http://www.eurandom.tue.nl/reports/2011/004-report.pd