FitEllipsoid: a fast supervised ellipsoid segmentation plugin

BMC Bioinformatics

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[1] 0000 0001 2353 1689, grid.11417.32, ITAV, CNRS, Université de Toulouse, 1 Pl. Pierre Potier, 31106, Toulouse, France;0000 0001 2353 1689, grid.11417.32, ITAV, CNRS, Université de Toulouse, 1 Pl. Pierre Potier, 31106, Toulouse, France;0000 0001 2353 1689, grid.11417.32, IMT, CNRS, Université de Toulouse, 118, route de Narbonne, 31400, Toulouse, France;

关键词: Supervised segmentation;    Ellipsoid;    Icy plugin;   

DOI  :  10.1186/s12859-019-2673-0

来源: publisher

【 摘 要 】

BackgroundThe segmentation of a 3D image is a task that can hardly be automatized in certain situations, notably when the contrast is low and/or the distance between elements is small. The existing supervised methods require a high amount of user input, e.g. delineating the domain in all planar sections.ResultsWe present FitEllipsoid, a supervised segmentation code that allows fitting ellipsoids to 3D images with a minimal amount of interactions: the user clicks on a few points on the boundary of the object on 3 orthogonal views. The quantitative geometric results of the segmentation of ellipsoids can be exported as a csv file or as a binary image. The core of the code is based on an original computational approach to fit ellipsoids to point clouds in an affine invariant manner. The plugin is validated by segmenting a large number of 3D nuclei in tumor spheroids, allowing to analyze the distribution of their shapes. User experiments show that large collections of nuclei can be segmented with a high accuracy much faster than with more traditional 2D slice by slice delineation approaches.ConclusionsWe designed a user-friendly software FitEllipsoid allowing to segment hundreds of ellipsoidal shapes in a supervised manner. It may be used directly to analyze biological samples, or to generate segmentation databases necessary to train learning algorithms. The algorithm is distributed as an open-source plugin to be used within the image analysis software Icy. We also provide a Matlab toolbox available with GitHub.

【 授权许可】

CC BY