The use of a multi-channel kalman filter algorithm in structural analysis of the epileptic EEG

An extension of the Kalman filter algorithm to the multi-channel case is presented and its application as a segmenting procedure in the analysis of the epileptic EEG is discussed. An analytical example of structural analysis, using the segments extracted by the proposed filter, is presented for a particular set of 4-channel EEG recordings. This analysis is shown to be especially fruitful if the autoregressive coefficients - a by product of the filtering procedure - are used to estimate the information flow between the channels by the calculation of partial as well as directed coherences for the representative segments.     

Segmentation of complex cell clusters in microscopic images: application to bone marrow samples.

BACKGROUND: Morphologic examination of bone marrow and peripheral blood samples continues to be the cornerstone in diagnostic hematology. In recent years, interest in automatic leukocyte classification using image analysis has increased rapidly. Such systems collect a series of images in which each cell must be segmented accurately to be classified correctly. Although segmentation algorithms have been developed for sparse cells in peripheral blood, the problem of segmenting the complex cell clusters characterizing bone marrow images is harder and has not been addressed previously. METHODS: We present a novel algorithm for segmenting clusters of any number of densely packed cells. The algorithm first oversegments the image into cell subparts. These parts are then assembled into complete cells by solving a combinatorial optimization problem in an efficient way. RESULTS: Our experimental results show that the algorithm succeeds in correctly segmenting densely clustered leukocytes in bone marrow images. CONCLUSIONS: The presented algorithm enables image analysis-based analysis of bone marrow samples for the first time and may also be adopted for other digital cytometric applications where separation of complex cell clusters is required.     

Some Formal Approaches to the Analysis of Kinetic Data in Terms of Linear Compartmental Systems

A formal approach to the routine analysis of kinetic data in terms of linear compartmental systems is presented. The methods of analysis are general in that they include much of the theory in common use, such as direct solution of differential equations, integral equations, transfer functions, fitting of data to sums of exponentials, matrix solutions, etc. The key to the formalism presented lies in the fact that a basic operational unit—called “compartment”—has been defined, in terms of which physical and mathematical models as well as input and output functions can be expressed. Additional features for calculating linear combinations of functions and for setting linear dependence relations between parameters add to the versatility of this method. The actual computations for the values of model parameters to yield a least squares fit of the data are performed on a digital computer. A general computer program was developed that permits the routine fitting of data and the evolution of models.     

Application of theoretical considerations to the analysis of ELISA data

Solid-phase immunoassays such as the ELISA are in routine use in many areas of biological research. Data from these assays are analyzed in a variety of ways, frequently without taking into account the immunochemical principles of the assay. The Reference Standard Method is often used and is suitable and convenient for obtaining concentration (or activity) values from the antigen-specific ELISA or spRIA, sandwich assays, and inhibition assays. The standard curve required for this method may be obtained by simple linear regression analysis of logarithmic or logitlogarithmic transformed data obtained from titration of the reference standard. The shape of the logarithmic plot of the reference standard provides information on the performance of the assay. Examining data from multiple dilutions of the samples is essential to assure that each titrates with the same slope as does the reference standard; the analysis routine must permit this comparison to be made. ELISANALYSIS is a program for the IBM PC which was developed to perform such analyses. It is presented here as a model, with sufficient information provided for the development of similar analytical routines by interested users. This approach to ELISA data analysis is presented as an alternative to complicated empirical curve-fitting systems and simple endpoint methods, which can be immunochemically misleading or, in some cases, even invalid. The consistent use of the described routines would encourage greater uniformity in the means of data interpretation and thereby enhance our understanding of immunobiology.     

Methods for the spiral Salmonella mutagenicity assay including specialized applications

An automated approach to bacterial mutagenicity testing - the spiral Salmonella assay - was developed to simplify testing and to reduce the labor and materials required to generate dose-responsive mutagenicity information. This document provides the reader with an overview of the spiral assay and a discussion of its application for examining the mutagenic potential of pure compounds, complex environmental mixtures, and interactive effects. Guidelines for performing a routine spiral assay are presented, and alternative test methods intended to overcome a variety of technical difficulties (such as restricted sample availability, sample viscosity or volatility, etc.) are recommended. Methods for the computerized analysis of data and the interpretation of results are discussed.     

Database of sentences of Croatian language

The aim of this paper is to investigate morphological and syntactical levels of sentences of Croatian Language. Morphological grammatical level is represented by 16 categories and 47 features with theirs value. Syntactical level is represented with constituent structure trees of sentences. Database has 1001 grammatical sentences of Croatian literature. Database of sentences is the result of theoretical research in computational linguistics. This study extends the analysis of the linguistic data in anthropology in Croatian. Access to database is through the Internet on the address: http://infoz.ffzg.hr/tepes.     

jClustering,an Open Framework for the Development of 4D Clustering Algorithms

We present jClustering, an open framework for the design of clustering algorithms in dynamic medical imaging. We developed this tool because of the difficulty involved in manually segmenting dynamic PET images and the lack of availability of source code for published segmentation algorithms. Providing an easily extensible open tool encourages publication of source code to facilitate the process of comparing algorithms and provide interested third parties with the opportunity to review code. The internal structure of the framework allows an external developer to implement new algorithms easily and quickly, focusing only on the particulars of the method being implemented and not on image data handling and preprocessing. This tool has been coded in Java and is presented as an ImageJ plugin in order to take advantage of all the functionalities offered by this imaging analysis platform. Both binary packages and source code have been published, the latter under a free software license (GNU General Public License) to allow modification if necessary.     

Conversion of linear histogram flow cytometry data to a logarithmic display

A routine is described that readily allows the rescaling of linear histographic data to a corresponding logarithmic histogram. This procedure significantly improves data display, particularly where a wide range in the measured parameter is encountered. The logarithmic scale displays peaks with band widths more proportional to their respective coefficients of variation than is the case in a linear display. Rescaling several linear histograms to a common logarithmic scale allows the combination of these linear data even though the linear ranges are different. This routine is presented as a program written in BASIC for execution on a microcomputer.     

Assessment of metabolic properties and kinetic parameters of methanogenic sludge by on-line methane production rate measurements

This report presents a new approach to studying the metabolic and kinetic properties of anaerobic sludge from single batch experiments. The two main features of the method are that the methane production is measured on-line with a relatively cheap system, and that the methane production data can be plotted as rate vs time curves. The case studies of specific methanogenic activity, biodegradability and toxicity tests here presented show that very accurate kinetic data can be obtained. The method is specifically useful in experiments in which strong changes in methane production occur, and it is proposed as a powerful tool to study methanogenic systems. Furthermore, the method is simple and could be implemented by industry in the routine analysis of sludge.     

Music and video iconicity: theory and experimental design

Experimental studies on the relationship between quasi-musical patterns and visual movement have largely focused on either referential, associative aspects or syntactical, accent-oriented alignments. Both of these are very important, however, between the referential and areferential lays a domain where visual pattern perceptually connects to musical pattern; this is iconicity. The temporal syntax of accent structures in iconicity is hypothesized to be important. Beyond that, a multidimensional visual space connects to musical patterning through mapping of visual time/space to musical time/magnitudes. Experimental visual and musical correlates are presented and comparisons to previous research provided.     

Ramp edges,Mach bands,and the functional significance of the simple cell assembly

The responses of “complex” simple cells to sharp and blurred ramp edges were studied. These responses are quite similar to those in the case of lines, which implies that phase information cannot be used to discriminate between ramp edges and lines. Furthermore, if the maximum of the modulus is used as a position estimate, a systematic bias toward the ramp side results, and this bias increases with edge blur. In contrast, a local extremum in the real part of the cell responses provides a precise position estimate, even for strongly blurred edges. Possible multiscale detection strategies are discussed in the context of a syntactical visual reconstruction. This is illustrated by an explanation of Mach bands as perceived at trapezoidal edges, including Ratliff’s Mach-band cancellation stimulus, and criteria for local probability summation in the prediction of Mach-band detection thresholds are presented. Received: 10 December 1992/Accepted in revised form: 6 August 1993     

Computer programs for the analysis and the management of DNA sequences.

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.     

Mechanisms underlying nutrient-induced segmentation in isolated guinea pig small intestine

Mechanisms underlying nutrient-induced segmentation within the gut are not well understood. We have shown that decanoic acid and some amino acids induce neurally dependent segmentation in guinea pig small intestine in vitro. This study examined the neural mechanisms underlying segmentation in the circular muscle and whether the timing of segmentation contractions also depends on slow waves. Decanoic acid (1 mM) was infused into the lumen of guinea pig duodenum and jejunum. Video imaging was used to monitor intestinal diameter as a function of both longitudinal position and time. Circular muscle electrical activity was recorded by using suction electrodes. Recordings from sites of segmenting contractions showed they are always associated with excitatory junction potentials leading to action potentials. Recordings from sites oral and anal to segmenting contractions revealed inhibitory junction potentials that were time locked to those contractions. Slow waves were never observed underlying segmenting contractions. In paralyzed preparations, intracellular recording revealed that slow-wave frequency was highly consistent at 19.5 (SD 1.4) cycles per minute (c/min) in duodenum and 16.6 (SD 1.1) c/min in jejunum. By contrast, the frequencies of segmenting contractions varied widely (duodenum: 3.6-28.8 c/min, median 10.8 c/min; jejunum: 3.0-27.0 c/min, median 7.8 c/min) and sometimes exceeded slow-wave frequencies for that region. Thus nutrient-induced segmentation contractions in guinea pig small intestine do not depend on slow-wave activity. Rather they result from a neural circuit producing rhythmic localized activity in excitatory motor neurons, while simultaneously activating surrounding inhibitory motor neurons.     

Condition-dependent functional connectivity: syntax networks in bilinguals

This paper introduces a method to study the variation of brain functional connectivity networks with respect to experimental conditions in fMRI data. It is related to the psychophysiological interaction technique introduced by Friston et al. and extends to networks of correlation modulation (CM networks). Extended networks containing several dozens of nodes are determined in which the links correspond to consistent correlation modulation across subjects. In addition, we assess inter-subject variability and determine networks in which the condition-dependent functional interactions can be explained by a subject-dependent variable. We applied the technique to data from a study on syntactical production in bilinguals and analysed functional interactions differentially across tasks (word reading or sentence production) and across languages. We find an extended network of consistent functional interaction modulation across tasks, whereas the network comparing languages shows fewer links. Interestingly, there is evidence for a specific network in which the differences in functional interaction across subjects can be explained by differences in the subjects' syntactical proficiency. Specifically, we find that regions, including ones that have previously been shown to be involved in syntax and in language production, such as the left inferior frontal gyrus, putamen, insula, precentral gyrus, as well as the supplementary motor area, are more functionally linked during sentence production in the second, compared with the first, language in syntactically more proficient bilinguals than in syntactically less proficient ones. Our approach extends conventional activation analyses to the notion of networks, emphasizing functional interactions between regions independently of whether or not they are activated. On the one hand, it gives rise to testable hypotheses and allows an interpretation of the results in terms of the previous literature, and on the other hand, it provides a basis for studying the structure of functional interactions as a whole, and hence represents a further step towards the notion of large-scale networks in functional imaging.     

Data transfer from Beckman LS 5800 liquid scintillation counters to IBM personal computers

This communication describes a short routine in BASICA for theIBM-PC, written to collect data from a Beckman liquid scintillationcounter. In the form presented here the routine converts incomingbytes into separate lines and saves these lines in a file. Thereare many possible applications for further use of the data inthese files. A few suggestions are given as to the format inwhich data can be stored and how to process these data automaticallyafter all samples have been counted. The only hardware neededis an asynchronous communications adapter for the IBM-PC andan RS232 cable. Received on July 27, 1985; accepted on August 2, 1985     

A computer program for the analysis of crossover designs.

We describe a program, CROSS, which we have written to obtain potency estimates and other parameters for bioassay data from assays of crossover design. The program permits testing of all assays for statistical validity and calculates the complete analysis of variance for assays of balanced design. The form of data input and the complete documentation of assay results make this program particularly useful for anyone carrying out crossover assays on a routine basis. The analysis of variance presented is also useful for more general biological or medical situations.     

Retinal Vessel Segmentation: An Efficient Graph Cut Approach with Retinex and Local Phase

Our application concerns the automated detection of vessels in retinal images to improve understanding of the disease mechanism, diagnosis and treatment of retinal and a number of systemic diseases. We propose a new framework for segmenting retinal vasculatures with much improved accuracy and efficiency. The proposed framework consists of three technical components: Retinex-based image inhomogeneity correction, local phase-based vessel enhancement and graph cut-based active contour segmentation. These procedures are applied in the following order. Underpinned by the Retinex theory, the inhomogeneity correction step aims to address challenges presented by the image intensity inhomogeneities, and the relatively low contrast of thin vessels compared to the background. The local phase enhancement technique is employed to enhance vessels for its superiority in preserving the vessel edges. The graph cut-based active contour method is used for its efficiency and effectiveness in segmenting the vessels from the enhanced images using the local phase filter. We have demonstrated its performance by applying it to four public retinal image datasets (3 datasets of color fundus photography and 1 of fluorescein angiography). Statistical analysis demonstrates that each component of the framework can provide the level of performance expected. The proposed framework is compared with widely used unsupervised and supervised methods, showing that the overall framework outperforms its competitors. For example, the achieved sensitivity (0:744), specificity (0:978) and accuracy (0:953) for the DRIVE dataset are very close to those of the manual annotations obtained by the second observer.     

In-depth analysis of tandem mass spectrometry data from disparate instrument types

Mass spectrometric analyses of protein digests produce large numbers of fragmentation spectra that are not identified by routine database searching strategies. Some of these spectra could be identified by development of improved search engines. However, many of these spectra represent fragmentation of peptide components bearing modifications that are not routinely considered in database searches. Here we present new software within Protein Prospector that allows comprehensive analysis of data sets by analyzing the data at increasing levels of depth. Analysis of published data sets is presented to illustrate that the software is not biased to any instrument types. The results show that these data sets contain many modified peptides. As well as searching for known modification types, Protein Prospector permits the detection and identification of unexpected or novel modifications by searching for any mass shift within a user-specified mass range to any chosen amino acid(s). Several modifications never previously reported in proteomics data were identified in these standard data sets using this mass modification searching approach.     

Enabling user-guided segmentation and tracking of surface-labeled cells in time-lapse image sets of living tissues

To study the process of morphogenesis, one often needs to collect and segment time-lapse images of living tissues to accurately track changing cellular morphology. This task typically involves segmenting and tracking tens to hundreds of individual cells over hundreds of image frames, a scale that would certainly benefit from automated routines; however, any automated routine would need to reliably handle a large number of sporadic, and yet typical problems (e.g., illumination inconsistency, photobleaching, rapid cell motions, and drift of focus or of cells moving through the imaging plane). Here, we present a segmentation and cell tracking approach based on the premise that users know their data best-interpreting and using image features that are not accounted for in any a priori algorithm design. We have developed a program, SeedWater Segmenter, that combines a parameter-less and fast automated watershed algorithm with a suite of manual intervention tools that enables users with little to no specialized knowledge of image processing to efficiently segment images with near-perfect accuracy based on simple user interactions.