1,721,113 research outputs found
Colour deconvolution: stain unmixing in histological imaging
Full text linkMOTIVATION: Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images digitally opens the possibility to process numerically colour distribution and intensity to extract quantitative data. Among those numerical procedures is colour deconvolution, which enables decomposing an RGB image into channels representing the optical absorbance and transmittance of the dyes when their RGB representation is known. Consequently, a range of new applications become possible for morphological and histochemical segmentation, automated marker localisation and image enhancement.AVAILABILITY AND IMPLEMENTATION: Colour deconvolution is presented here in two open-source forms: a MATLAB program/function and an ImageJ plugin written in Java. Both versions run in Windows, Macintosh, and UNIX-based systems under the respective platforms. Source code and further documentation are available at: https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online
Nuclear morphometry and ploidy of normal and neoplastic haemocytes in mussels
Full text linkHaemic neoplasia (HN) in bivalves has been reported in association with mass mortality events in various species of molluscs. The aim of this work was to quantify the nuclear morphometry and DNA content of neoplastic cells of mussels Mytilus galloprovincialis affected by HN using nuclear densitometry in Feulgen-stained preparations. The results were also compared with a population of normal mussel haemocytes. We captured 256 images of 3 different neoplasia stages and 120 images of normal haemocytes; thus, a total of 120,166 nuclei were analysed. We extracted 21 morphological parameters from normal and neoplastic nuclei. Eighteen of these parameters were different (P<0.05). Among those (expressed in pixel units-inter-pixel distance of 0.45 micrometres-as: normal vs. neoplastic) nuclear area (117.1±94.1 vs. 423.1±226.9), perimeter (44.9±14.0 vs. 79.0±21.3) and (IOD) integrated optical density (13.47±34.5 vs. 177.1±150.8) were relevant features to discriminate between normal and neoplastic cells. Those differences allowed identifying two distinctive populations of neoplastic nuclei, occasionally in the same individuals at a given phase of the disease. Moreover, neoplastic haemocytes in less extended lesions showed a ploidy value of 6.2 n along with the presence of a second population of circulating cells with a DNA content of 10.7n. In samples with moderate disease only one peak at 7n was observed. Finally, in more severe conditions, a further ploidy peak of 7.8n was recorded, accompanied by a shallow but broad peak of 31n. This latter extreme value is thought to be due to the presence of giant multinucleated cells where individual nuclei overlap in space and cannot be discerned individually. Computer-based imaging allowed the direct visualization of the cell populations and simultaneous collection of ploidy data as well as morphological features of nuclei
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Identifying plant species using architectural features in leaf microscopy images
Full text linkThis work proposes an analytical method to identify plant species based on microscopy images of the midrib cross-section of leaves. Unlike previous shape-based approaches based on the individual shape of external contours and cells, an architectural analysis is proposed, where the midrib is semi-automatically segmented and partitioned into histologically relevant structures composed of layers of cells and vascular structures. Using a sequence of morphological operations, a set of geometrical measures from the cells in each layer is extracted to produce a vector of features for species categorization. The method applied to a database containing 10 species of plants from the Brazilian flora achieved a success rate of 91.7%, outperforming other classical shape-based approaches published in the literature.Fil: Florindo, Joao Batista. Universidade de Sao Paulo; BrasilFil: Bruno, Odemir Martinez. Universidade de Sao Paulo; BrasilFil: Rossatto, Davi Rodrigo. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Kolb, Rosana Marta. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Gómez, María Cecilia. Universidad Nacional del Litoral; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Landini, Gabriel. University Of Birmingham; Reino Unid
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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