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 number 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 less detailed 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 a too large 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, from Drosophila pupa and  chicken embryo; the pipeline results are robust. Perspectives include  tissues, non-biological cellular patterns such as foams, and 3D images .
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, non-biological cellular patterns such as foams, and xyz stacks .
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number
numbers
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less detailed
coarse grained
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a too large
too large a
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Transform based
transform-based
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the other from a
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in vitro
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3D images
xyz stacks