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Fast determination of coarse-grained cell anisotropy and size in epithelial tissue images using Fourier transform

Abstract : Mechanical strain and stress play a major role in biological processes such as wound healing or morphogenesis. To assess this role quantitatively, fixed or live images of tissues are acquired at a cellular precision in large fields of views. To exploit these data, large numbers of cells have to be analyzed to extract cell shape anisotropy and cell size. Most frequently, this is performed through detailed individual cell contour determination, using so-called segmentation computer programs, complemented if necessary by manual detection and error corrections. However, a coarse-grained and faster technique can be recommended in at least three situations: first, when detailed information on individual cell contours is not required; for instance, in studies which require only coarse-grained average information on cell anisotropy. Second, as an exploratory step to determine whether full segmentation can be potentially useful. Third, when segmentation is too difficult, for instance due to poor image quality or too large a cell number. We developed a user-friendly, Fourier-transform-based image analysis pipeline. It is fast (typically $10^4$ cells per minute with a current laptop computer) and suitable for time, space, or ensemble averages. We validate it on one set of artificial images and on two sets of fully segmented images, one from a Drosophila pupa and the other from a chicken embryo; the pipeline results are robust. Perspectives include in vitro tissues, nonbiological cellular patterns such as foams and $xyz$ stacks.
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https://hal-univ-lyon1.archives-ouvertes.fr/hal-02367869
Contributor : Armelle Vidal <>
Submitted on : Monday, November 18, 2019 - 11:13:03 AM
Last modification on : Wednesday, September 2, 2020 - 3:22:50 AM

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Mélina Durande, S. Tlili, T. Homan, B. Guirao, F. Graner, et al.. Fast determination of coarse-grained cell anisotropy and size in epithelial tissue images using Fourier transform. Physical Review E , American Physical Society (APS), 2019, 99 (6), pp.062401. ⟨10.1103/PhysRevE.99.062401⟩. ⟨hal-02367869⟩

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