ArticleBioinformatics (Oxford, England)2021
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity.Cell reports · 2025Article
- TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging.Genome biology · 2025Article
- Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics.Nature communications · 2025Article
- TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging.bioRxiv : the preprint server for biology · 2025Article
- Label and quantify mRNA molecules in live cell experiments using SunRISER and dNEMO.STAR protocols · 2022Article
- Long-term imaging of individual mRNA molecules in living cells.Cell reports methods · 2022Article
- A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-κB.Science advances · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationMany biological processes are regulated by single molecules and molecular assemblies within cells that are visible by microscopy as punctate features, often diffraction limited. Here, we present detecting-NEMO (dNEMO), a computational tool optimized for accurate and rapid measurement of fluorescent puncta in fixed-cell and time-lapse images.
resultsThe spot detection algorithm uses the à trous wavelet transform, a computationally inexpensive method that is robust to imaging noise. By combining automated with manual spot curation in the user interface, fluorescent puncta can be carefully selected and measured against their local background to extract high-quality single-cell data. Integrated into the workflow are segmentation and spot-inspection tools that enable almost real-time interaction with images without time consuming pre-processing steps. Although the software is agnostic to the type of puncta imaged, we demonstrate dNEMO using smFISH to measure transcript numbers in single cells in addition to the transient formation of IKK/NEMO puncta from time-lapse images of cells exposed to inflammatory stimuli. We conclude that dNEMO is an ideal user interface for rapid and accurate measurement of fluorescent molecular assemblies in biological imaging data. AVAILABILITY AND IMPLEMENTATION: The data and software are freely available online at https://github.com/recleelab. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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