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 a parallel implementation of a watershed algorithm is proposed. The algorithm can easily be implemented on shared memory parallel computers. The watershed transform is generally considered to be inherently sequential since the discrete watershed of an image is defined using recursion. However, recently a few research groups, have designed parallel algorithms for computing watersheds. Most of these parallel algorithms are based on splitting the source image in blocks, computing the watershed of these blocks and merging the resulting images into the desired result. A disadvantage of this approach is that a lot of communication is necessary at the boundaries of the blocks. In this paper we show that it is possible to transform the computation of the discrete watershed into a sequence of three simple steps which are easier to execute in parallel than the original algorithm. In the first step the input image is transformed into a graph representation of the image. In the second step we compute the watershed of this graph and finally we transform the resulting graph back into the image domain.

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Arnold Meijster

Papers

An Alternative Algorithm for Computing Watersheds on Shared Memory Parallel Computers

High performance computing and networking, proceedings