Quantitative evaluation of the shapes of biological organs is often required in various research fields, such as agronomy, medicine, genetics, ecology, and taxonomy. Elliptic Fourier descriptors (EFDs), proposed by Kuhl and Giardina (1982), can delineate any type of shape with a closed two-dimensional contour and have been effectively applied to the evaluation of various biological shapes in animals (Bierbaum and Ferson 1986; Diaz et al. 1989; Ferson et al. 1985; Rohlf and Archie 1984) and plants (Furuta et al. 1995; Iwata et al. 1998; McLellan 1993; Ohsawa et al. 1998; White et al. 1988). Quantization of shapes is a prerequisite for evaluating the inheritance of morphological traits in quantitative genetics. There are many reports showing that measurements based on EFDs are helpful for such quantization of the shapes of plant and animal organs. For instance, Iwata et al. (2000) conducted a diallele analysis of the shape of Japanese radish (Raphanus sativus L.) roots, using the principal component scores of the EFDs as shape characteristics. Quantitative trait loci (QTL) analysis has also been conducted using the principal component scores of EFDs concerning the shape of the male genitalia of Drosophila species (Laurie et al. 1997; Liu et al. 1996). The shape evaluation method based on EFDs can be a powerful tool for analyzing biological shapes, but it is not easy for a researcher to use this method because it involves several complex procedures, such as image processing, contour recording, derivation of the descriptors, and multivariate analysis of the descriptors. In this article we present SHAPE, a package of programs for evaluating biological contour shapes based on EFDs. This package contains programs for image processing, contour recording, derivation of EFDs, principal component analysis of EFDs, and visualization of shape variations estimated by the principal components. With the aid of this package, a researcher can easily analyze shapes on a personal computer without special knowledge about the procedures related to the method. The principal component scores obtained by the procedures can be used directly as observed values of shape characteristics for the subsequent analyses. SHAPE is characterized by the following features: (1) The packaged programs are easily operated with the aid of a graphical user interface (GUI); (2) No special computer devices for image processing are required; (3) A large number of samples (say 1,000) can be treated; (4) The scores of principal components are stored in tabbed text format files and can be easily exported for analysis by other software; and (5) The variations in shape accounted for by the principal components can be visualized and printed out.

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SHAPE: A Computer Program Package for Quantitative Evaluation of Biological Shapes Based on Elliptic Fourier Descriptors

Lamins A and C but not lamin B1 regulate nuclear mechanics

Emery-Dreifuss muscular dystrophy can be caused by mutations in the nuclear envelope proteins lamin A/C and emerin. We recently demonstrated that A-type lamin-deficient cells have impaired nuclear mechanics and altered mechanotransduction, suggesting two potential disease mechanisms (Lammerding, J., P.C. Schulze, T. Takahashi, S. Kozlov, T. Sullivan, R.D. Kamm, C.L. Stewart, and R.T. Lee. 2004. J. Clin. Invest. 113:370–378). Here, we examined the function of emerin on nuclear mechanics and strain-induced signaling. Emerin-deficient mouse embryo fibroblasts have abnormal nuclear shape, but in contrast to A-type lamin-deficient cells, exhibit nuclear deformations comparable to wild-type cells in cellular strain experiments, and the integrity of emerin-deficient nuclear envelopes appeared normal in a nuclear microinjection assay. Interestingly, expression of mechanosensitive genes in response to mechanical strain was impaired in emerin-deficient cells, and prolonged mechanical stimulation increased apoptosis in emerin-deficient cells. Thus, emerin-deficient mouse embryo fibroblasts have apparently normal nuclear mechanics but impaired expression of mechanosensitive genes in response to strain, suggesting that emerin mutations may act through altered transcriptional regulation and not by increasing nuclear fragility.

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Abnormal nuclear shape and impaired mechanotransduction in emerin-deficient cells

From the Publisher:
Image Processing Handbook covers methods for two different purposes:
Improving the visual appearance of images to a human viewerPreparing images for measurement of the features and structures present.

The handbook presents an extensive collection of image processing tools, enabling the user of computer-based system to understand those methods provided in packaged software and to program additions needed for particular applications. Comparisons are presented of different algorithms that may be used for similar purposes, including a selection of representative pictures from light and electron microscopes as well as macroscopic, satellite, and astronomical images.
Image Processing Handbook examines the rapid, powerful developments in graphic information, covering the array of concepts and techniques in high-end imaging software. With balanced, complete descriptions, the text outlines frequency space methods with extensive mathematical presentation and spatial domain processing. This handbook teaches by example -- by seeing what various operations do to representative images, the reader will discover how and why to use them. The text encourages the reader to use its information with a real source of images and a computer-based system as well as to freely experiment with different methods to determine the most appropriate for his or her particular needs.To facilitate the learning process, Reindeer Games in Charlotte, North Carolina, offers The Image Processing Tool Kit, a CD-ROM containing more than 150 images and more than 150 Photoshop-compatible plug-ins that implement the algorithms discussed. This revision of the established standard acts as a singular resource for professionals in the medical, biological, and materials sciences as well as a range of engineering venues, including electrical and computer engineering, optical engineering, telecommunications, and artificial intelligence.

Image Processing Handbook, Fourth Edition

Whether obtained by microscopes, space probes, or the human eye, the same basic tools can be applied to acquire, process, and analyze the data contained in images Ideal for self study, The Image Processing Handbook, Sixth Edition, first published in 1992, raises the bar once again as the gold-standard reference on this subject Using extensive new illustrations and diagrams, it offers a logically organized exploration of the important relationship between two-dimensional images and the three-dimensional structures they reveal Provides Hundreds of Visual Examples in FULL COLOR! The author focuses on helping readers visualize and compare processing and measurement operations and how they are typically combined in fields ranging from microscopy and astronomy to real-world scientific, industrial, and forensic applications Presenting methods in the order in which they would be applied in a typical workflowfrom acquisition to interpretationthis book compares a wide range of algorithms used to: Improve the appearance, printing, and transmission of an image Prepare images for measurement of the features and structures they reveal Isolate objects and structures, and measure their size, shape, color, and position Correct defects and deal with limitations in images Enhance visual content and interpretation of details This handbook avoids dense mathematics, instead using new practical examples that better convey essential principles of image processing This approach is more useful to develop readers grasp of how and why to apply processing techniques and ultimately process the mathematical foundations behind them Much more than just an arbitrary collection of algorithms, this is the rare book that goes beyond mere image improvement, presenting a wide range of powerful example images that illustrate techniques involved in color processing and enhancement Applying his 50-year experience as a scientist, educator, and industrial consultant, John Russ offers the benefit of his image processing expertise for fields ranging from astronomy and biomedical research to food science and forensics His valuable insights and guidance continue to make this handbook a must-have reference

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A. Ghiani

Papers

Elliptic fourier analysis of cell and nuclear shapes