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Biomedical subjects

L da F Costa

Publications and source records attributed to L da F Costa.

5 recordsLinked to original sources

Complex networks approach to gene expression driven phenotype imaging.

MOTIVATION: The need is to visualize and quantify gene expression spatial patterns. Because of their generality for representation of interaction among several elements, complex networks are used to measure the spatial interactions and adjacencies defined by gene expression patterns. RESULTS: Enhanced visualization of spatial interactions between elements where genes are expressed is possible, allowing the identification of structures which would go unnoticed by using conventional imaging. The quantification of the expression intensity in terms of the node degree and clustering coefficient allows the identification of different types of interactions, yielding insights about cell signaling and differentiation, and providing the basis for comparison and discrimination of the patterns along the developmental stages. AVAILABILITY: Supplementary Material, including visualizations as well as the basic routines for translating gene expression images into complex networks and obtaining node degree and clustering coefficient measurements, are provided. CONTACT: luciano@if.sc.usp.br; diambra@univap.br.

Algorithms↗

Mathematical characterization of three-dimensional gene expression patterns.

MOTIVATION: The importance of a systematic methodology for the mathematical characterization of three-dimensional gene expression patterns in embryonic development. METHODS: By combining lacunarity and multiscale fractal dimension analyses with computer-based methods of three-dimensional reconstruction, it becomes possible to extract new information from in situ hybridization studies. Lacunarity and fractality are appropriate measures for the cloud-like gene activation signals in embryonic tissues. The newly introduced multiscale method provides a natural extension of the fractal dimension concept, being capable of characterizing the fractality of geometrical patterns in terms of spatial scale. This tool can be systematically applied to three-dimensional patterns of gene expression. RESULTS: Applications are illustrated using the three-dimensional expression patterns of the myogenic marker gene Myf5 in a series of differentiating somites of a mouse embryo.

Animals↗

A computational approach to characterization of bovine sperm chromatin alterations.

We describe here a computational morphology-based approach to the investigation of possible causes of chromatin alterations in sperm. A comprehensive set of state-of-the-art and geometric measures are computationally extracted from toluidine blue stained images and analyzed to infer the possible processes leading to normal and abnormal chromatin formation while seeking a possible taxonomy of chromatin alterations and their influence on sperm head morphology. Using this methodology, we have identified higher chromatin fragility at some specific points of the sperm head. Despite the lack of correlation between morphologies of sperm head and chromatin structure, four main morphological types of chromatin alterations in bull spermatozoa have been identified and their possible causes discussed.

Animals↗

Automatic characterization and classification of ganglion cells from the salamander retina.

The classification of retinal ganglion cells according to their morphological features is addressed by using a comprehensive set of shape measures and several clustering strategies. The morphological features considered include many common measures (such as dendritic radii and the number of dendritic segments) and three new quantifiable measures: 1) the area of influence of the dendritic tree as calculated in an operator-independent manner by using Minkowski sausages; 2) the complexity of tortuousity along each dendritic segment as represented by the 3D bending energy; and 3) the coverage factor as calculated by using the Bouligand-Minkowski fractal dimension, which is more accurate than the commonly used box-counting algorithm. We evaluated four clustering approaches including the k-means and Ward's hierarchical clustering methods. By using these highly quantifiable methods to group the cells into classes, the present work has extended and reassessed the analysis of 68 ganglion cells from the tiger salamander previously classified by Toris et al. ([1995] J. Comp. Neurol. 352:535-559). Though substantiating the number of classes (5) previously proposed by Toris et al., the results obtained here indicate a number of discrepancies among the members of each class, especially regarding the border between two classes, originally called the medium simple and the medium complex cells. Such an effect has motivated the proposal of new names for the medium simple and medium complex classes, now called small highly complex and medium cells, respectively. Also included in the present article are comprehensive statistics of each class, correlations among all the adopted shape measures, and examples of the cells from each class. The resultant classes that emerged were compared using their electrotonic characteristics and physiological profiles.

Ambystoma↗

Neural cell classification by wavelets and multiscale curvature.

A new approach to automatic classification of retinal ganglion cells using multiscale techniques including the continuous wavelet transform, curvature, and standard pattern recognition techniques is described. Each neural cell is represented by its outer contour, and the wavelet transform is calculated from the complex signal defined by the aforementioned contour, leading to the so-called W-representation (Antoine et al. 1996). The normalized multiscale wavelet energy (NMWE) is used to define a set of shape measures associated with the number of details of the shape for a broad range of spatial scales. Next, the more discriminating NMWE coefficients are chosen through a feature ordering technique and fed to statistical classifiers. In addition, the normalized multiscale bending energy (NMBE) is discussed as a means of neural shape description for classification purposes based on the multiscale curvature, i.e. the curvegram, of the neural contour. It is shown that both shape descriptors are suitable for shape classification, presenting similar classification performance. In fact, NMBE has a slightly better recognition rate than NMWE in our experiments. On the other hand, NMWE is less computationally expensive than NMBE, presenting also the potentially useful property of allowing the use of more suitable different analyzing wavelets, depending on the problem under consideration. Therefore, both measures are related and provide a good framework for the design of neural cell description and classification. The methods described in this work have been successfully applied to the classification of two classes of cat retinal ganglion cells, namely alpha and beta (henceforth referred as alpha-cells and beta-cells, respectively), and three statistical classifiers were considered: minimum-distance, k-nearest neighbours and maximum likelihood. The mean recognition rates are near 90%, which is superior to the other shape measures considered. It is argued here that the proposed technique can be adopted as a new general methodology for multiscale shape analysis and recognition, being applicable also to other problems in biological shape characterization in neuroscience and general biomedical image analysis. In the context of analysis of shape complexity, the multiscale energies are coherent with subjective judgements by humans.

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