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.

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Contour Detection and Hierarchical Image Segmentation

Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.

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Using circular dichroism spectra to estimate protein secondary structure

A generic preprocessing method for multivariate data, called orthogonal projections to latent structures (O-PLS), is described. O-PLS removes variation from X (descriptor variables) that is not correlated to Y (property variables, e.g. yield, cost or toxicity). In mathematical terms this is equivalent to removing systematic variation in X that is orthogonal to Y. In an earlier paper, Wold et al. (Chemometrics Intell. Lab. Syst. 1998; 44: 175-185) described orthogonal signal correction (OSC). In this paper a method with the same objective but with different means is described. The proposed O-PLS method analyzes the variation explained in each PLS component. The non-correlated systematic variation in X is removed, making interpretation of the resulting PLS model easier and with the additional benefit that the non-correlated variation itself can be analyzed further. As an example, near-infrared (NIR) reflectance spectra of wood chips were analyzed. Applying O-PLS resulted in reduced model complexity with preserved prediction ability, effective removal of non-correlated variation in X and, not least, improved interpretational ability of both correlated and non-correlated variation in the NIR spectra.

Orthogonal projections to latent structures (O-PLS)

Pre-processing of near-infrared (NIR) spectral data has become an integral part of chemometrics modeling. The objective of the pre-processing is to remove physical phenomena in the spectra in order to improve the subsequent multivariate regression, classification model or exploratory analysis. The most widely used pre-processing techniques can be divided into two categories: scatter-correction methods and spectral derivatives. This review describes and compares the theoretical and algorithmic foundations of current pre-processing methods plus the qualitative and quantitative consequences of their application. The aim is to provide NIR users with better end-models through fundamental knowledge on spectral pre-processing.

Review of the most common pre-processing techniques for near-infrared spectra

Respiration effects and cardiac pulsatility can induce signal modulations in functional MR image time series that increase noise and degrade the statistical significance of activation signals. A simple image-based correction method is described that does not have the limitations of k-space methods that preclude high spatial frequency correction. Low-order Fourier series are fit to the image data based on time of each image acquisition relative to the phase of the cardiac and respiratory cycles, monitored using a photoplethysmograph and pneumatic belt, respectively. The RETROICOR method is demonstrated using resting-state experiments on three subjects and compared with the k-space method. The method is found to perform well for both respiration- and cardiac-induced noise without imposing spatial filtering on the correction. Magn Reson Med 44:162‐167, 2000. © 2000 Wiley-Liss, Inc.

/pdf/image-based-method-for-retrospective-correction-of-19044i2hn4.pdf

Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR.

In a method and apparatus for two-dimensional parallel data processing, a pattern of information to be analyzed is reproduced in a field of bi-stable information bearing elements. The pattern is processed by comparing the states of the six nearest neighbor elements around each element with at least one of the possible patterns of states of said six neighbor elements, without regard to correspondence of rotational orientation of the actual pattern with the possible patterns, and fixing each element in a predetermined state when the actual pattern of states of its six neighbors matches a selected one or more of the possible patterns. The predetermined state in which each element is placed may be a function of the states of its six neighbors, a function of its own original state and the states of its six neighbors, or its own original state. In order that the state of an element be fixed in relation to the original states of its six nearest neighbors, and not in relation to new states of the neighbors resulting from the processing, the field is adapted to be processed by designating subfield groups of three, four or seven elements in which no two adjacent elements in the field are in the same subfield and then by processing the respective subfield groups in succession. In a preferred form each element of the field consists of a line of subelements with the corresponding subelements of different elements being arranged in layers, such that the several layers of subelements are homologous. The subelements in each layer are interconnected with each other and with the corresponding subelements (of the same element) in the other layers, and each subelement of each layer is connected to control elements including an input data reader, an instruction bank, an evaluation unit and a program unit. The processing may thus include fixing subelements of one layer respectively in states which are functions of corresponding subelements in other layers.

Analysis of images

Previous results on skewsymmetric sequences with low autocorrelation obtained by making exhaustive searches for sequences with optimal merit factor are extended up to length 69 A sieve that required both the symmetric and antisymmetric components of a skewsymmetric sequence to have high merit factor to make limited searches up to length 117 was used, and many sequences with merit factor greater than 9 were found >

A new search for skewsymmetric binary sequences with optimal merit factors

An improved field homogenizing coil arrangement of a type having a generally tubular coil form extending about a test sample in an NMR apparatus is described. The coil arrangement includes a plurality of separate coils which are orthogonally related and which are formed of conductive segments positioned on opposite surfaces of the coil form and are conductively coupled through the form. The coils include arcuate-shaped segments positioned on one surface of the form and aligned normally with respect to a main polarizing field component, and rectilinear shaped segments positioned on an opposite surface of the form and extending in a direction substantially parallel to the main polarizing field component. The conductive segments are fabricated on the form by printed circuit techniques and the form is adapted to be rolled into a scroll-shaped configuration. With this arrangement, a relatively large number of field corrective coils are positioned on the form while overlapping rectilinear segments cancel undesired fields established by current return paths.

Nuclear magnetic resonance apparatus

Height equivalent to a thoretical plate of an open tubular column lined with a porous layer

J. Friend and E. Watson have suggested that if an adequate ‘performance index’ could be defined for gas chromatographic columns, a much-needed clarification could be achieved in the interchange of data among experimenters.

Marcel J. E. Golay

Papers

Analysis of images

A new search for skewsymmetric binary sequences with optimal merit factors

Nuclear magnetic resonance apparatus

Height equivalent to a thoretical plate of an open tubular column lined with a porous layer

A Performance Index for Gas Chromatographic Columns