Zusammenfassung
We introduce a 3D model-based approach for automatic segmentation of 3D fluorescent heterochromatin foci from 3D microscopy images. The approach employs a new 3D parametric intensity model based on a spherical harmonics (SH) expansion and can represent foci of regular and highly irregular shapes. By solving a least-squares optimization problem, the model is directly fitted to the 3D image data, and the model parameters including the SH expansion coefficients are estimated. The approach has been successfully applied to real 3D microscopy image data. A visual comparison and a quantitative evaluation show that the new approach yields better results than previous approaches.
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Literatur
Ivashkevich AN, Martin OA, Smith AJ, et al. H2AX foci as a measure of DNA damage: a computational approach to automatic analysis. Mutat Res. 2011;711(1–2):49–60.
Dzyubachyk O, Essers J, van Cappellen WA, et al. Automated analysis of timelapse fluorescence microscopy images: from live cell images to intracellular foci. Bioinformatics. 2010;26(19):2424–30.
Thomann D, Rines DR, Sorger PK, et al. Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement. J Microscopy. 2002;208:49–64.
Wörz S, Sander P, Pfannmöller M, et al. 3D geometry-based quantification of colocalizations in multichannel 3D microscopy images of human soft tissue tumors. IEEE Trans Med Imaging. 2010;29(8):1474–84.
Eck S, Rohr K, Müller-Ott K, et al. Combined model-based and region-adaptive 3D segmentation and 3D co-localization analysis of heterochromatin foci. Proc BVM. 2012; p. 9–14.
Székely G, Kelemen A, Brechbühler C, et al. Segmentation of 2-D and 3-D objects from MRI volume data using constrained elastic deformations of flexible Fourier contour and surface models. Med Image Anal. 1996;1(1):19–34.
Arfken GB, Weber HJ, Harris FE. Mathematical Methods for Physicists. Sixth ed. Academic Press; 2005.
El-Baz A, Nitzken M, Khalifa F, et al. 3D shape analysis for early diagnosis of malignant lung nodules. Lect Notes Comput Sci. 2011;6801:772–83.
Shen L, Firpi HA, Saykin AJ, et al. Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. Hippocampus. 2009;19(6):588–95.
Baust M, Navab N. A spherical harmonics shape model for level set segmentation. Lect Notes Comput Sci. 2010;6313:580–93.
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© 2013 Springer-Verlag Berlin Heidelberg
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Eck, S., Wörz, S., Biesdorf, A., Müller-Ott, K., Rippe, K., Rohr, K. (2013). Segmentation of Heterochromatin Foci Using a 3D Spherical Harmonics Intensity Model. In: Meinzer, HP., Deserno, T., Handels, H., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2013. Informatik aktuell. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36480-8_54
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DOI: https://doi.org/10.1007/978-3-642-36480-8_54
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Online ISBN: 978-3-642-36480-8
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