ArticleNature communications2016
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review of generative adversarial networks (GANs) in cell microscopy: Trends, practices, and impact on image augmentation.PloS one · 2025Pooled it
- Unsupervised spatiotemporal classification of deformation patterns of embryonic tissues matches their fate map.iScience · 2025Article
- Coupling of cell shape, matrix and tissue dynamics ensures embryonic patterning robustness.Nature cell biology · 2025Article
- Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets.PLoS computational biology · 2024Article
- nAdder: A scale-space approach for the 3D analysis of neuronal traces.PLoS computational biology · 2022Article
- Delineating the mechanisms and design principles ofComputational and structural biotechnology journal · 2022Review
- Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis.Bioinformatics (Oxford, England) · 2021Article
- Synthetic living machines: A new window on life.iScience · 2021Review
- From Cell States to Cell Fates: How Cell Proliferation and Neuronal Differentiation Are Coordinated During Embryonic Development.Frontiers in neuroscience · 2021Review
- Article
- Tools and Concepts for Interrogating and Defining Cellular Identity.Cell stem cell · 2020Review
- Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures.PLoS biology · 2019Article
- Cdh2 coordinates Myosin-II dependent internalisation of the zebrafish neural plate.Scientific reports · 2019Article
- Quantitative analysis of cell shape and the cytoskeleton in developmental biology.Wiley interdisciplinary reviews. Developmental biology · 2018Review
- Three-dimensional microscopy and image analysis methodology for mapping and quantification of nuclear positions in tissues with approximate cylindrical geometry.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Control of the proportion of inner cells by asymmetric divisions and the ensuing resilience of cloned rabbit embryos.Development (Cambridge, England) · 2018Article
- EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.PLoS computational biology · 2018Article
- Article
- Image analysis of neural stem cell division patterns in the zebrafish brain.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2018Article
- Deciphering tissue morphodynamics using bioimage informatics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
Corrections and comments
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Authors and funding
31 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology.
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