ArticleNature methods2014
Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
136 citing papers in PubMed.
- Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration.Nature physics · 2026Article
- Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation.Molecular systems biology · 2026Article
- NucVerse3D: generalizable 3D nuclear instance segmentation across heterogeneous microscopy modalities.Scientific reports · 2026Article
- Positional information and information flows in dynamic tissues.bioRxiv : the preprint server for biology · 2026Article
- EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation.bioRxiv : the preprint server for biology · 2026Article
- High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction.bioRxiv : the preprint server for biology · 2026Article
- CellMigrationGym: a data-driven framework utilizing deep reinforcement learning to unravel mechanisms of cell migration.BMC proceedings · 2026Article
- Methods to analyze cell migration data: fundamentals and practical guidelines.Nature methods · 2026Review
- Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation.bioRxiv : the preprint server for biology · 2025Article
- Ultrack: pushing the limits of cell tracking across biological scales.Nature methods · 2025Article
- inTRACKtive: a web-based tool for interactive cell tracking visualization.Nature methods · 2025Article
- Universal consensus 3D segmentation of cells from 2D segmented stacks.Nature methods · 2025Article
- In toto live imaging of Erk signaling dynamics in developing zebrafish hepatocytes.Developmental biology · 2025Article
- LivecellX: A Scalable Deep Learning Framework for Single-Cell Object-Oriented Analysis in Live-Cell Imaging.bioRxiv : the preprint server for biology · 2025Article
- Unsupervised spatiotemporal classification of deformation patterns of embryonic tissues matches their fate map.iScience · 2025Article
- Genetically encoded tension heterogeneity sculpts cardiac trabeculation.Science advances · 2025Article
- DeepKymoTracker: A tool for accurate construction of cell lineage trees for highly motile cells.PloS one · 2025Article
- Cell dynamics revealed by microscopy advances.Current opinion in cell biology · 2024Review
- CMTT-JTracker: a fully test-time adaptive framework serving automated cell lineage construction.Briefings in bioinformatics · 2024Article
- Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research.Microscopy (Oxford, England) · 2024Review
76 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terabyte-sized image data sets of fruit fly, zebrafish and mouse embryos acquired with three types of fluorescence microscopes, (ii) scalability by analyzing advanced stages of development with up to 20,000 cells per time point at 26,000 cells min(-1) on a single computer workstation and (iii) ease of use by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities. Using our system, we performed the first cell lineage reconstruction of early Drosophila melanogaster nervous system development, revealing neuroblast dynamics throughout an entire embryo.
Indexed as
Identifiers
25042785What OpenQuestion holds
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.