ArticleNucleus (Austin, Tex.)2022
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes.
Article in Nucleus (Austin, Tex.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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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Who cites it
11 citing papers in PubMed.
- Sex chromosome pairing and multivalent associations during meiosis in diploid and polyploid Silene latifolia.Plant physiology · 2026Article
- Loss of E3 ligase HvST1 function substantially increases distal crossover frequency.The New phytologist · 2026Article
- From cells to pixels: A decision tree for designing bioimage analysis pipelines.Journal of microscopy · 2025Article
- Thriving or Withering? Plant Molecular Cytogenetics in the First Quarter of the 21st Century.International journal of molecular sciences · 2025Review
- Connecting high-resolution 3D chromatin maps with cell division and cell differentiation at the root apical meristem.Plant cell reports · 2024Article
- Fluorescent carbon nanodot-based rapid cell nucleus staining and application for diagnosis.Journal of food and drug analysis · 2024Article
- The holocentricity in the dioecious nutmeg (Myristica fragrans) is not based on major satellite repeats.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Article
- An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains.Molecular cell · 2024Article
- Insight into chromatin compaction and spatial organization in rice interphase nuclei.Frontiers in plant science · 2024Article
- Meiotic segregation and post-meiotic drive of the Festuca pratensis B chromosome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- The art of painting chromosome loops.Quantitative plant biology · 2023Article
Corrections and comments
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Authors and funding
23 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.
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Registered trials
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