Dataset Information

Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.

ABSTRACT: One of the most important and error-prone tasks in biological image analysis is the segmentation of touching or overlapping cells. Particularly for optical microscopy, including transmitted light and confocal fluorescence microscopy, there is often no consistent discriminative information to separate cells that touch or overlap. It is desired to partition touching foreground pixels into cells using the binary threshold image information only, and optionally incorporating gradient information. The most common approaches for segmenting touching and overlapping cells in these scenarios are based on the watershed transform. We describe a new approach called pixel replication for the task of segmenting elliptical objects that touch or overlap. Pixel replication uses the image Euclidean distance transform in combination with Gaussian mixture models to better exploit practically effective optimization for delineating objects with elliptical decision boundaries. Pixel replication improves significantly on commonly used methods based on watershed transforms, or based on fitting Gaussian mixtures directly to the thresholded image data. Pixel replication works equivalently on both 2-D and 3-D image data, and naturally combines information from multi-channel images. The accuracy of the proposed technique is measured using both the segmentation accuracy on simulated ellipse data and the tracking accuracy on validated stem cell tracking results extracted from hundreds of live-cell microscopy image sequences. Pixel replication is shown to be significantly more accurate compared with other approaches. Variance relationships are derived, allowing a more practically effective Gaussian mixture model to extract cell boundaries for data generated from the threshold image using the uniform elliptical distribution and from the distance transform image using the triangular elliptical distribution.

SUBMITTER: Winter M

PROVIDER: S-EPMC6450753 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.

Winter Mark M Mankowski Walter W Wait Eric E De La Hoz Edgar Cardenas EC Aguinaldo Angeline A Cohen Andrew R AR

IEEE transactions on medical imaging 20181005 4

One of the most important and error-prone tasks in biological image analysis is the segmentation of touching or overlapping cells. Particularly for optical microscopy, including transmitted light and confocal fluorescence microscopy, there is often no consistent discriminative information to separate cells that touch or overlap. It is desired to partition touching foreground pixels into cells using the binary threshold image information only, and optionally incorporating gradient information. Th ...[more]

PMID: 30296216

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Project description:European and American minks (Mustela lutreola and Neovison vison, respectively) are very similar in their ecology, behavior, and morphology. However, the American mink is a generalist predator and seems to adapt better to anthropized environments, allowing it to outcompete the European mink in areas where it has been introduced, threatening the survival of the native species. To assess whether morphological differences may be contributing to the success of the American mink relative to the European mink, we analyzed shape variation in the cranium of both species using 3D geometric morphometrics. A set of 38 landmarks and 107 semilandmarks was used to study shape variation between and within species, and to assess how differences in size factored into that variation. Sexual dimorphism in both size and shape was also studied. Significant differences between species were found in cranial shape, but not in size. Relative to American mink, European mink have a shorter facial region with a rounder forehead and wider orbits, a longer neurocranium with less developed crests and processes, and an antero-medially placed tympanic bullae with an anteriorly expanded cranial border. Within species, size-related sexual dimorphism is highly significant, but sexual dimorphism in shape is only significant in American mink, not in European mink. Additionally, two trends common to both species were discovered, one related to allometric changes and another to sexual size dimorphism. Shape changes related to increasing size can be subdivided into two, probably related, groups: increased muscle force and growth. The first group somewhat parallels the differences between both mink species, while the second group of traits includes an anterodorsal expansion of the face, and the neurocranium shifting from a globous shape in small individuals to a dorsoventrally flattened ellipse in the largest ones. Finally, the sexual dimorphism trend, while also accounting for differences in muscle force, seems to be related to the observed dietary differences between males and females. Overall, differences between species and sexes, and shape changes with increasing size, seem to mainly relate to differences in masticatory-muscle volume and therefore muscle force and bite force, which, in turn, relate to a wider range of potential prey (bigger prey, tougher shells). Thus, muscle force (and dietary range) would be larger in American mink than in European mink, in males than in females, and in larger individuals than in smaller ones.

Dataset Information

Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.

Publications

Separating Touching Cells Using Pixel Replicated Elliptical Shape Models.

Similar Datasets

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