{"version":1,"kind":"Article","sha256":"","slug":"321","location":"","dependencies":[],"doi":"10.54294/8est51","thumbnail":"https://pub.desci.com/ipfs/bafkreicbbvyqzbiwtbqcegiyd6luwiszstpdidkkprjhctdn3o6wwgkzxu","frontmatter":{"title":"Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours","abstract":"An Insight Toolkit (ITK) processing framework for blob segmentation with applications to microscopy \r\nimages is presented in this paper. Our algorithm is a refinement of the work of Mosaliganti et al. [3] for \r\nsplitting cell clusters. The basic idea is to incorporate as many cues as possible into developing a suitable \r\nlevel-set speed function so that an evolving contour exactly segments a cell/nuclei blob. We use image \r\ngradients, distance maps, multiple channel information and a shape model to drive the evolution. The \r\nframework consists of a linear pipeline of 6 new ITK filters which are applied in succession to generate \r\nthe segmentation. The filters extract the cell foreground, construct the speed image, find seed points for \r\nevolution and collect cell statistics from the segmentation. We include 2D/3D example code, parameter \r\nsettings and show the results generated on confocal images of the zebrafish embryo.","license":"You are licensing your work to Kitware Inc. under the\nCreative Commons Attribution License Version 3.0.\n\nKitware Inc. agrees to the following:\n\nKitware is free\n * to copy, distribute, display, and perform the work\n * to make derivative works\n * to make commercial use of the work\n\nUnder the following conditions:\n\\\"by Attribution\\\" - Kitware must attribute the work in the manner specified by the author or licensor.\n\n * For any reuse or distribution, they must make clear to others the license terms of this work.\n * Any of these conditions can be waived if they get permission from the copyright holder.\n\nYour fair use and other rights are in no way affected by the above.\n\nThis is a human-readable summary of the Legal Code (the full license) available at\nhttp://creativecommons.org/licenses/by/3.0/legalcode","keywords":["geodesic active contour ","Microscopy","segmentation"],"authors":[{"name":"Mosaliganti, kishore","email":"kishoreraom@gmail.com","affiliations":[]},{"name":"gelas, arnaud","email":"arnaudgelas@gmail.com","affiliations":[]},{"name":"gouaillard, alexandre","email":"agouaillard@gmail.com","affiliations":["Singapore Agency for Science Technology and Research"],"corresponding":true},{"name":"Megason, Sean","affiliations":[]}],"date_submitted":"2009-03-11 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