PUBLICATION
Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification
- Authors
- Wu, T.C., Wang, X., Li, L., Bu, Y., Umulis, D.M.
- ID
- ZDB-PUB-210512-5
- Date
- 2021
- Source
- Scientific Reports 11: 9847 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Algorithms
- Animals
- Cell Nucleus*
- Developmental Biology/methods*
- Embryo, Nonmammalian/diagnostic imaging
- Imaging, Three-Dimensional/methods*
- Intravital Microscopy/methods*
- Models, Animal
- Signal-To-Noise Ratio
- Spatio-Temporal Analysis
- Zebrafish
- PubMed
- 33972575 Full text @ Sci. Rep.
Citation
Wu, T.C., Wang, X., Li, L., Bu, Y., Umulis, D.M. (2021) Automatic wavelet-based 3D nuclei segmentation and analysis for multicellular embryo quantification. Scientific Reports. 11:9847.
Abstract
Identification of individual cells in tissues, organs, and in various developing systems is a well-studied problem because it is an essential part of objectively analyzing quantitative images in numerous biological contexts. We developed a size-dependent wavelet-based segmentation method that provides robust segmentation without any preprocessing, filtering or fine-tuning steps, and is robust to the signal-to-noise ratio. The wavelet-based method achieves robust segmentation results with respect to True Positive rate, Precision, and segmentation accuracy compared with other commonly used methods. We applied the segmentation program to zebrafish embryonic development IN TOTO for nuclei segmentation, image registration, and nuclei shape analysis. These new approaches to segmentation provide a means to carry out quantitative patterning analysis with single-cell precision throughout three dimensional tissues and embryos and they have a high tolerance for non-uniform and noisy image data sets.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping