PUBLICATION
CytoCensus, mapping cell identity and division in tissues and organs using machine learning
- Authors
- Hailstone, M., Waithe, D., Samuels, T.J., Yang, L., Costello, I., Arava, Y., Robertson, E., Parton, R.M., Davis, I.
- ID
- ZDB-PUB-200520-3
- Date
- 2020
- Source
- eLIFE 9: (Journal)
- Registered Authors
- Keywords
- 3D cell detection, 4D image analysis, D. melanogaster, cell biology, developmental biology, ex vivo culture, live imaging, mouse, neural stem cells, zebrafish
- MeSH Terms
-
- Animals
- Animals, Genetically Modified
- Automation
- Brain/embryology
- Cell Division*
- Drosophila melanogaster/embryology
- Drosophila melanogaster/genetics
- Embryo, Mammalian/cytology
- Female
- Image Processing, Computer-Assisted*
- Larva/cytology
- Machine Learning*
- Male
- Mice
- Microscopy, Video*
- Mutation
- Organoids/cytology
- Phenotype
- Reproducibility of Results
- Retina/cytology
- Time Factors
- Time-Lapse Imaging*
- Tissue Culture Techniques
- Zebrafish
- PubMed
- 32423529 Full text @ Elife
Citation
Hailstone, M., Waithe, D., Samuels, T.J., Yang, L., Costello, I., Arava, Y., Robertson, E., Parton, R.M., Davis, I. (2020) CytoCensus, mapping cell identity and division in tissues and organs using machine learning. eLIFE. 9:.
Abstract
A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends convenient 2D 'point-and-click' user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection. We used CytoCensus to count stem cells and their progeny, and to quantify individual cell divisions from time-lapse movies of explanted Drosophila larval brains, comparing wild-type and mutant phenotypes. We further illustrate the general utility and future potential of CytoCensus by analysing the 3D organisation of multiple cell classes in Zebrafish retinal organoids and cell distributions in mouse embryos. CytoCensus opens the possibility of straightforward and robust automated analysis of developmental phenotypes in complex tissues.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping