PUBLICATION
Object Segmentation and Ground Truth in 3D Embryonic Imaging
- Authors
- Bhavna, R., Uriu, K., Valentin, G., Tinevez, J.Y., Oates, A.C
- ID
- ZDB-PUB-170720-19
- Date
- 2016
- Source
- PLoS One 11: e0150853 (Journal)
- Registered Authors
- Oates, Andrew
- Keywords
- Algorithms, Embryos, Imaging techniques, Morphogenic segmentation, Zebrafish, Image processing, Image analysis, Signal to noise ratio
- MeSH Terms
-
- Algorithms*
- Animals
- Cell Nucleus
- Chimerism
- Embryo, Nonmammalian/anatomy & histology*
- Imaging, Three-Dimensional*
- Zebrafish/embryology*
- PubMed
- 27332860 Full text @ PLoS One
Citation
Bhavna, R., Uriu, K., Valentin, G., Tinevez, J.Y., Oates, A.C (2016) Object Segmentation and Ground Truth in 3D Embryonic Imaging. PLoS One. 11:e0150853.
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.
Errata / Notes
This article is corrected by ZDB-PUB-220906-49.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping