PUBLICATION
Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos
- Authors
- Stegmaier, J., Amat, F., Lemon, W.C., McDole, K., Wan, Y., Teodoro, G., Mikut, R., Keller, P.J.
- ID
- ZDB-PUB-160127-3
- Date
- 2016
- Source
- Developmental Cell 36: 225-240 (Journal)
- Registered Authors
- Amat, Fernando, Keller, Philipp, Lemon, William, Mikut, Ralf, Wan, Yinan
- Keywords
- none
- MeSH Terms
-
- Algorithms
- Animals
- Cell Shape/physiology*
- Cell Tracking/methods
- Drosophila
- Embryonic Development/physiology*
- Imaging, Three-Dimensional
- Mice
- Microscopy, Fluorescence/methods
- Software
- Zebrafish
- PubMed
- 26812020 Full text @ Dev. Cell
Citation
Stegmaier, J., Amat, F., Lemon, W.C., McDole, K., Wan, Y., Teodoro, G., Mikut, R., Keller, P.J. (2016) Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos. Developmental Cell. 36:225-240.
Abstract
We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55-330 times faster and 2-5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from entire Drosophila, zebrafish, and mouse embryos imaged with confocal and light-sheet microscopes. Using RACE, we automatically reconstructed cellular-resolution tissue anisotropy maps across developing Drosophila embryos and quantified differences in cell-shape dynamics in wild-type and mutant embryos. We furthermore integrated RACE with our framework for automated cell lineaging and performed joint segmentation and cell tracking in entire Drosophila embryos. RACE processed these terabyte-sized datasets on a single computer within 1.4 days. RACE is easy to use, as it requires adjustment of only three parameters, takes full advantage of state-of-the-art multi-core processors and graphics cards, and is available as open-source software for Windows, Linux, and Mac OS.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping