ArticleDevelopment (Cambridge, England)2012
Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos.
Article in Development (Cambridge, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation.Bioinformatics (Oxford, England) · 2020Pooled it
- Heritable epigenetic changes are constrained by the dynamics of regulatory architectures.eLife · 2024Article
- Article
- Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy.Genetics · 2022Review
- Delineating the mechanisms and design principles ofComputational and structural biotechnology journal · 2022Review
- Computational modeling and analysis of the morphogenetic domain signaling networks regulatingComputational and structural biotechnology journal · 2022Article
- Using Live Imaging to Examine Early Cardiac Development in Zebrafish.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Attractive internuclear force drives the collective behavior of nuclear arrays in Drosophila embryos.PLoS computational biology · 2021Article
- Article
- Speciation and the developmental alarm clock.eLife · 2020Review
- Game of Tissues: How the Epidermis ThronesJournal of developmental biology · 2020Review
- Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans.Lab animal · 2019Review
- Sample path properties of the average generation of a Bellman-Harris process.Journal of mathematical biology · 2019Article
- A high-content imaging approach to profileDevelopment (Cambridge, England) · 2019Article
- Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis.Bioinformatics (Oxford, England) · 2018Article
- EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.PLoS computational biology · 2018Article
- A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo.PloS one · 2018Article
- Automated C. elegans embryo alignments reveal brain neuropil position invariance despite lax cell body placement.PloS one · 2018Article
- Revealing chiral cell motility by 3D Riesz transform-differential interference contrast microscopy and computational kinematic analysis.Nature communications · 2017Article
- Biologically constrained optimization based cell membrane segmentation in C. elegans embryos.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.