ArticlePLoS computational biology2018
EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research.Microscopy (Oxford, England) · 2024Review
- Topology-based segmentation of 3D confocal images of emerging hematopoietic stem cells in the zebrafish embryo.Biological imaging · 2024Article
- u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions.Cell reports methods · 2023Article
- CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages.BMC bioinformatics · 2023Article
- Scents from the past: Lineage history and terminal identity in the olfactory system.Natural sciences (Weinheim, Germany) · 2022Article
- LiveCellMiner: A new tool to analyze mitotic progression.PloS one · 2022Article
- Ventral striatal islands of Calleja neurons control grooming in mice.Nature neuroscience · 2021Article
- A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction.PloS one · 2021Article
- Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.PLoS genetics · 2020Article
- Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy.PloS one · 2020Article
- Ontology patterns for the representation of quality changes of cells in time.Journal of biomedical semantics · 2019Article
- MorphoNet: an interactive online morphological browser to explore complex multi-scale data.Nature communications · 2019Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.
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