ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying

International audienceBackground. Over the last two decades, an innovative technology called Tissue Microarray (TMA),which combines multi-tissue and DNA microarray concepts, has been widely used in the field ofhistology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembledonto a single support – typically a glass slide – according to a design grid (array) layout, in order toallow multiplex analysis by treating numerous samples under identical and standardized conditions.However, during the TMA manufacturing process, the sample positions can be highly distorted fromthe design grid due to the imprecision when assembling tissue samples and the deformation of theembedding waxes. Consequently, these distortions may lead to severe errors of (histological) assayresults when the sample identities are mismatched between the design and its manufactured output.The development of a robust method for de-arraying TMA, which localizes and matches TMAsamples with their design grid, is therefore crucial to overcome the bottleneck of this prominenttechnology.Results. In this paper, we propose an Automatic, fast and robust TMA De-arraying (ATMAD)approach dedicated to images acquired with bright field and fluorescence microscopes (or scanners).First, tissue samples are localized in the large image by applying a locally adaptive thresholdingon the isotropic wavelet transform of the input TMA image. To reduce false detections, a parametricshape model is considered for segmenting ellipse-shaped objects at each detected position.Segmented objects that do not meet the size and the roundness criteria are discarded from thelist of tissue samples before being matched with the design grid. Sample matching is performed byestimating the TMA grid deformation under the thin-plate model. Finally, thanks to the estimateddeformation, the true tissue samples that were preliminary rejected in the early image processingstep are recognized by running a second segmentation step.Conclusions. We developed a novel de-arraying approach for TMA analysis. By combining waveletbaseddetection, active contour segmentation, and thin-plate spline interpolation, our approach isable to handle TMA images with high dynamic, poor signal-to-noise ratio, complex background andnon-linear deformation of TMA grid. In addition, the deformation estimation produces quantitativeinformation to asset the manufacturing quality of TMAs

Efficient Local Comparison Of Images Using Krawtchouk Descriptors

It is known that image comparison can prove cumbersome in both computational complexity and runtime, due to factors such as the rotation, scaling, and translation of the object in question. Due to the locality of Krawtchouk polynomials, relatively few descriptors are necessary to describe a given image, and this can be achieved with minimal memory usage. Using this method, not only can images be described efficiently as a whole, but specific regions of images can be described as well without cropping. Due to this property, queries can be found within a single large image, or collection of large images, which serve as a database for search. Krawtchouk descriptors can also describe collections of patches of 3D objects, which is explored in this paper, as well as a theoretical methodology of describing nD hyperobjects. Test results for an implementation of 3D Krawtchouk descriptors in GNU Octave, as well as statistics regarding effectiveness and runtime, are included, and the code used for testing will be published open source in the near future

Microarray image processing: A novel neural network framework

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.Aleppo University, Syri

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

<p>Abstract</p> <p>Background</p> <p>Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the underlying structure of these natural datasets is often fuzzy, and the computational identification of data clusters generally requires knowledge about cluster number and geometry.</p> <p>Results</p> <p>We integrated strategies from machine learning, cartography, and graph theory into a new informatics method for automatically clustering self-organizing map ensembles of high-dimensional data. Our new method, called AutoSOME, readily identifies discrete and fuzzy data clusters without prior knowledge of cluster number or structure in diverse datasets including whole genome microarray data. Visualization of AutoSOME output using network diagrams and differential heat maps reveals unexpected variation among well-characterized cancer cell lines. Co-expression analysis of data from human embryonic and induced pluripotent stem cells using AutoSOME identifies >3400 up-regulated genes associated with pluripotency, and indicates that a recently identified protein-protein interaction network characterizing pluripotency was underestimated by a factor of four.</p> <p>Conclusions</p> <p>By effectively extracting important information from high-dimensional microarray data without prior knowledge or the need for data filtration, AutoSOME can yield systems-level insights from whole genome microarray expression studies. Due to its generality, this new method should also have practical utility for a variety of data-intensive applications, including the results of deep sequencing experiments. AutoSOME is available for download at <url>http://jimcooperlab.mcdb.ucsb.edu/autosome</url>.</p

On Multilabel Classification Methods of Incompletely Labeled Biomedical Text Data

Multilabel classification is often hindered by incompletely labeled training datasets; for some items of such dataset (or even for all of them) some labels may be omitted. In this case, we cannot know if any item is labeled fully and correctly. When we train a classifier directly on incompletely labeled dataset, it performs ineffectively. To overcome the problem, we added an extra step, training set modification, before training a classifier. In this paper, we try two algorithms for training set modification: weighted k-nearest neighbor (WkNN) and soft supervised learning (SoftSL). Both of these approaches are based on similarity measurements between data vectors. We performed the experiments on AgingPortfolio (text dataset) and then rechecked on the Yeast (nontext genetic data). We tried SVM and RF classifiers for the original datasets and then for the modified ones. For each dataset, our experiments demonstrated that both classification algorithms performed considerably better when preceded by the training set modification step

Applications of MATLAB in Science and Engineering

The book consists of 24 chapters illustrating a wide range of areas where MATLAB tools are applied. These areas include mathematics, physics, chemistry and chemical engineering, mechanical engineering, biological (molecular biology) and medical sciences, communication and control systems, digital signal, image and video processing, system modeling and simulation. Many interesting problems have been included throughout the book, and its contents will be beneficial for students and professionals in wide areas of interest

Advanced Image Acquisition, Processing Techniques and Applications

"Advanced Image Acquisition, Processing Techniques and Applications" is the first book of a series that provides image processing principles and practical software implementation on a broad range of applications. The book integrates material from leading researchers on Applied Digital Image Acquisition and Processing. An important feature of the book is its emphasis on software tools and scientific computing in order to enhance results and arrive at problem solution