title: Object Segmentation and Ground Truth in 3D Embryonic Imaging.
abstract: Many questions in developmental biology depend on measuring the position and movement of individual cells within developing embryos. Yet, tools that provide this data are often challenged by high cell density and their accuracy is difficult to measure. Here, we present a three-step procedure to address this problem. Step one is a novel segmentation algorithm based on image derivatives that, in combination with selective post-processing, reliably and automatically segments cell nuclei from images of densely packed tissue. Step two is a quantitative validation using synthetic images to ascertain the efficiency of the algorithm with respect to signal-to-noise ratio and object density. Finally, we propose an original method to generate reliable and experimentally faithful ground truth datasets: Sparse-dense dual-labeled embryo chimeras are used to unambiguously measure segmentation errors within experimental data. Together, the three steps outlined here establish a robust, iterative procedure to fine-tune image analysis algorithms and microscopy settings associated with embryonic 3D image data sets.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
authors.forename: Bhavna
authors.initials: B
authors.lastname: Rajasekaran
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.|Theoretical Biology Laboratory, RIKEN, Saitama, Japan.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Uriu
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|MRC-National Institute for Medical Research, London, United Kingdom.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Valentin
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Tinevez
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|MRC-National Institute for Medical Research, London, United Kingdom.|Department of Cell and Developmental Biology, University College, London, United Kingdom.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Oates
mesh_terms: D000465:Algorithms; D000818:Animals; D002467:Cell Nucleus; D046528:Chimerism; D004625:Embryo, Nonmammalian / Q000033:anatomy & histology*; D021621:Imaging, Three-Dimensional; D015027:Zebrafish / Q000196:embryology*