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.

A guided tour into subcellular colocalization analysis in light microscopy

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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The watershed transform: definitions, algorithms and parallelization strategies

Digital inpainting provides a means for reconstruction of small damaged portions of an image. Although the inpainting basics are straightforward, most inpainting techniques published in the literature are complex to understand and implement. We present here a new algorithm for digital inpainting based on the fast marching method for level set applications. Our algorithm is very simple to implement, fast, and produces nearly identical results to more complex, and usually slower, known methods. Source code is available online.

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An Image Inpainting Technique Based on the Fast Marching Method

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.

Improved watershed transform for medical image segmentation using prior information

Morphological attribute profiles (APs) are defined as a generalization of the recently proposed morphological profiles (MPs). APs provide a multilevel characterization of an image created by the sequential application of morphological attribute filters that can be used to model different kinds of the structural information. According to the type of the attributes considered in the morphological attribute transformation, different parametric features can be modeled. The generation of APs, thanks to an efficient implementation, strongly reduces the computational load required for the computation of conventional MPs. Moreover, the characterization of the image with different attributes leads to a more complete description of the scene and to a more accurate modeling of the spatial information than with the use of conventional morphological filters based on a predefined structuring element. Here, the features extracted by the proposed operators were used for the classification of two very high resolution panchromatic images acquired by Quickbird on the city of Trento, Italy. The experimental analysis proved the usefulness of APs in modeling the spatial information present in the images. The classification maps obtained by considering different APs result in a better description of the scene (both in terms of thematic and geometric accuracy) than those obtained with an MP.

Morphological Attribute Profiles for the Analysis of Very High Resolution Images

In this paper the implementation of a watershed transform based on Tarjan's Union-Find algorithm is described. The algorithm computes the watershed as defined by Meyer in [4]. The algorithm consists of two stages. In the first stage the image to be segmented is transformed into a lower complete image, using a FIFO-queue algorithm. In the second stage, the watershed of the lower complete image is computed. In this stage no FIFO-queues are used. This feature makes parallel implementation of the watershed transform much easier.

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A disjoint set algorithm for the watershed transform

In this paper a parallel implementation of a watershed algorithm is proposed. The algorithm is designed for a ring-architecture with distributed memory and a piece of shared memory using a single program multiple data (SPMD) approach. The watershed transform is generally considered to be inherently sequential. This paper shows that it is possible to exploit parallelism by splitting the computation of the watersheds of an image into three stages that can be executed in parallel.

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A Proposal for the Implementation of a Parallel Watershed Algorithm

In this paper we describe a novel extension of the support vector machine, called the deep support vector machine (DSVM). The original SVM has a single layer with kernel functions and is therefore a shallow model. The DSVM can use an arbitrary number of layers, in which lower-level layers contain support vector machines that learn to extract relevant features from the input patterns or from the extracted features of one layer below. The highest level SVM performs the actual prediction using the highest-level extracted features as inputs. The system is trained by a simple gradient ascent learning rule on a min-max formulation of the optimization problem. A two-layer DSVM is compared to the regular SVM on ten regression datasets and the results show that the DSVM outperforms the SVM.

/pdf/deep-support-vector-machines-for-regression-problems-4fbjt7y90b.pdf

Deep Support Vector Machines for Regression Problems

This paper describes a new machine learning algorithm for regression and dimensionality reduction tasks. The Neural Support Vector Machine (NSVM) is a hybrid learning algorithm consisting of neural networks and support vector machines (SVMs). The output of the NSVM is given by SVMs that take a central feature layer as their input. The feature-layer representation is the output of a number of neural networks that are trained to minimize the dual objectives of the SVMs. Because the NSVM uses a shared feature layer, the learning architecture is able to handle multiple outputs and therefore it can also be used as a dimensionality reduction method. The results on 7 regression datasets show that the NSVM in general outperforms a standard SVM and a multi-layer perceptron. Furthermore, experiments on eye images show that the NSVM autoencoder outperforms state-of-the-art dimensionality reduction methods.

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Arnold Meijster

Papers

A disjoint set algorithm for the watershed transform

A Proposal for the Implementation of a Parallel Watershed Algorithm

Deep Support Vector Machines for Regression Problems

The Neural Support Vector Machine

The Watershed Transform