Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

This paper investigates two fundamental problems in computer vision: contour detection and image segmentation. We present state-of-the-art algorithms for both of these tasks. Our contour detector combines multiple local cues into a globalization framework based on spectral clustering. Our segmentation algorithm consists of generic machinery for transforming the output of any contour detector into a hierarchical region tree. In this manner, we reduce the problem of image segmentation to that of contour detection. Extensive experimental evaluation demonstrates that both our contour detection and segmentation methods significantly outperform competing algorithms. The automatically generated hierarchical segmentations can be interactively refined by user-specified annotations. Computation at multiple image resolutions provides a means of coupling our system to recognition applications.

/pdf/contour-detection-and-hierarchical-image-segmentation-2ejknw01zo.pdf

Contour Detection and Hierarchical Image Segmentation

2 1 The innovative transport systems and the CityMobil project 10 1.1 The research questions 10 2 The state of art in the field of automatic transport systems 12 2.1 Case studies and demand studies for innovative transport systems 12 3 The design and implementation of surveys 14 3.1 Definition of experimental design 14 3.2 Questionnaire design and delivery 16 3.3 First analyses on the collected sample 18 4 Calibration of Logit Multionomial demand models 21 4.1 Methodology 21 4.2 Calibration of the “full” model. 22 4.3 Calibration of the “final” model 24 4.4 The demand analysis through the final Multinomial Logit model 25 5 The analysis of interaction between the demand and socioeconomic attributes 31 5.1 Methodology 31 5.2 Application of Mixed Logit models to the demand 31 5.3 Analysis of the interactions between demand and socioeconomic attributes through Mixed Logit models 32 5.4 Mixed Logit model and interaction between age and the demand for the CTS 38 5.5 Demand analysis with Mixed Logit model 39 6 Final analyses and conclusions 45 6.1 Comparison between the results of the analyses 45 6.2 Conclusions 48 6.3 Answers to the research questions and future developments 52

The European commission

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

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

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.

/pdf/the-watershed-transform-definitions-algorithms-and-19vbswqg8k.pdf

The watershed transform: definitions, algorithms and parallelization strategies

A technique is described that is used to improve the detection of radio-frequency interference in astronomical radio observatories It is applied on a two-dimensional interference mask after regular detection in the time-frequency domain with existing techniques The scale-invariant rank (SIR) operator is defined, which is a one-dimensional mathematical morphology technique that can be used to find adjacent intervals in the time or frequency domain that are likely to be affected by RFI The technique might also be applicable in other areas in which morphological scale-invariant behaviour is desired, such as source detection A new algorithm is described, that is shown to perform quite well, has linear time complexity and is fast enough to be applied in modern high resolution observatories It is used in the default pipeline of the LOFAR observatory

https://www.aanda.org/articles/aa/pdf/2012/03/aa18497-11.pdf

A morphological algorithm for improving radio-frequency interference detection

A new general algorithm for computing distance transforms of digital images is presented. The algorithm consists of two phases. Both phases consist of two scans, a forward and a backward scan. The first phase scans the image column-wise, while the second phase scans the image row-wise. Since the computation per row (column) is independent of the computation of other rows (columns), the algorithm can be easily parallelized on shared memory computers. The algorithm can be used for the computation of the exact Euclidean, Manhattan (L 1 norm), and chessboard distance (L ∞ norm) transforms.

/pdf/a-general-algorithm-for-computing-distance-transforms-in-3lyswng46h.pdf

A general algorithm for computing distance transforms in linear time

We present a general wavelet-based denoising scheme for functional magnetic resonance imaging (fMRI) data and compare it to Gaussian smoothing, the traditional denoising method used in fMRI analysis. One-dimensional WaveLab thresholding routines were adapted to two-dimensional (2-D) images, and applied to 2-D wavelet coefficients. To test the effect of these methods on the signal-to-noise ratio (SNR), we compared the SNR of 2-D fMRI images before and after denoising, using both Gaussian smoothing and wavelet-based methods. We simulated a fMRI series with a time signal in an active spot, and tested the methods on noisy copies of it. The denoising methods were evaluated in two ways: by the average temporal SNR inside the original activated spot, and by the shape of the spot detected by thresholding the temporal SNR maps. Denoising methods that introduce much smoothness are better suited for low SNRs, but for images of reasonable quality they are not preferable, because they introduce heavy deformations. Wavelet-based denoising methods that introduce less smoothing preserve the sharpness of the images and retain the original shapes of active regions. We also performed statistical parametric mapping on the denoised simulated time series, as well as on a real fMRI data set. False discovery rate control was used to correct for multiple comparisons. The results show that the methods that produce smooth images introduce more false positives. The less smoothing wavelet-based methods, although generating more false negatives, produce a smaller total number of errors than Gaussian smoothing or wavelet-based methods with a large smoothing effect.

/pdf/denoising-functional-mr-images-a-comparison-of-wavelet-1grvw8q6xl.pdf

Denoising functional MR images: a comparison of wavelet denoising and Gaussian smoothing

In this paper, we describe a multiscale and multishape morphological method for pattern-based analysis and classification of gray-scale images using connected operators. Compared with existing methods, which use structuring elements, our method has three advantages. First, in our method, the time needed for computing pattern spectra does not depend on the number of scales or shapes used, i.e., the computation time is independent of the dimensions of the pattern spectrum. Second, size and strict shape attributes can be computed, which we use for the construction of joint 2D shape-size pattern spectra. Third, our method is significantly less sensitive to noise and is rotation-invariant. Although rotation invariance can also be approximated by methods using structuring elements at different angles, this tends to be computationally intensive. The classification performance of these methods is discussed using four image sets: Brodatz, COIL-20, COIL-100, and diatoms. The new method obtains better or equal classification performance to the best competitor with a 5 to 9-fold speed gain

/pdf/connected-shape-size-pattern-spectra-for-rotation-and-scale-mocktw0o1m.pdf

Jos B. T. M. Roerdink

Papers

The watershed transform: definitions, algorithms and parallelization strategies

A morphological algorithm for improving radio-frequency interference detection

A general algorithm for computing distance transforms in linear time

Denoising functional MR images: a comparison of wavelet denoising and Gaussian smoothing

Connected Shape-Size Pattern Spectra for Rotation and Scale-Invariant Classification of Gray-Scale Images