UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Object Segmentation and Ground Truth in 3D Embryonic Imaging

Rajasekaran, B; Uriu, K; Valentin, G; Tinevez, J-Y; Oates, AC; (2016) Object Segmentation and Ground Truth in 3D Embryonic Imaging. PLOS ONE , 11 (6) , Article e0150853. 10.1371/journal.pone.0150853. Green open access

[img]
Preview
Text
journal.pone.0150853.PDF - Published version

Download (3MB) | Preview

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.

Type: Article
Title: Object Segmentation and Ground Truth in 3D Embryonic Imaging
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0150853
Publisher version: http://dx.doi.org/10.1371/journal.pone.0150853
Additional information: © 2016 Rajasekaran et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Cell and Developmental Biology
URI: https://discovery.ucl.ac.uk/id/eprint/1503766
Downloads since deposit
70Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item