Deciphering tissue morphodynamics using bioimage informatics

@article{Dufour2017DecipheringTM,
  title={Deciphering tissue morphodynamics using bioimage informatics},
  author={Alexandre C. Dufour and Anneliene H. Jonker and Jean-Christophe Olivo-Marin},
  journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
  year={2017},
  volume={372}
}
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References

SHOWING 1-10 OF 69 REFERENCES
Tracking in cell and developmental biology.
Quantitative 4D analyses of epithelial folding during Drosophila gastrulation
TLDR
EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data, is developed and demonstrated that it enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo.
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
TLDR
The BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data is presented, achieving the best lineage score.
Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart
TLDR
An automated framework for the segmentation of 3D microscopy images of highly cluttered environments such as developing tissues is proposed based on a partial differential equation framework that jointly takes advantage of the nuclear and cellular membrane information to enable accurate extraction of nuclei and cells in dense tissues.
Simulating Organogenesis
TLDR
This work develops and evaluates different landmark-free algorithms for the determination of displacement fields from image data and concludes that in most cases, the normal distance algorithm is the method of choice and wherever it fails, diffusion-based mapping provides a good alternative.
$3D+t$ Morphological Processing: Applications to Embryogenesis Image Analysis
TLDR
The proposed processing paradigm produces spatio-temporal coherent results as it benefits from the intrinsic redundancy of the temporal dimension, and minimizes the needs for human intervention in semi-automatic algorithms.
ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
TLDR
By using the ACME software to study somite formation, the method was able to segment touching cells with high accuracy and reliably quantify changes in morphogenetic parameters such as cell shape and size, and the arrangement of epithelial and mesenchymal cells.
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images
TLDR
High-throughput 3D segmentation makes it possible to extract rich information from images that are routinely acquired by biologists, and provides insights — in particular with respect to the cell cycle — that would be difficult to derive otherwise.
...
...