ArticleThe European physical journal. E, Soft matter2021
CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images.
Article in The European physical journal. E, Soft matter, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Cilia SubQ: a modular suite of semi- and fully automated pipelines for analysis of primary cilia and ciliary subdomains.Methods (San Diego, Calif.) · 2026Article
- Three-dimensional approaches to measuring primary cilia in hippocampal neurons: A comparative analysis.Journal of neuropathology and experimental neurology · 2026Article
- Design principles of a membrane-spanning ubiquitin ligase.Molecular cell · 2026Article
- Modelling kidney cystogenesis using human kidney tubuloid cultures.BMC molecular and cell biology · 2026Article
- Cilia SubQ, a modular suite of pipelines for automated analysis of primary cilia and ciliary subdomains.bioRxiv : the preprint server for biology · 2026Article
- Primary cilia in the hypothalamic AgRP neurons mediate metabolic effects of butyrate.Nature communications · 2026Article
- Analysis of Primary Cilium-Bearing Human Neuroprogenitors Using Flow Cytometry.Stem cells international · 2026Article
- Article
- An enzymatic cascade enables sensitive and specific proximity labeling proteomics in challenging biological systems.Nature communications · 2025Article
- CEP76 impairment at the centrosome-cilium interface contributes to a spectrum of ciliopathies.Science advances · 2025Article
- CEP290 deficiency disrupts ciliary axonemal architecture in human iPSC-derived brain organoids.Journal of cell science · 2025Article
- A conserved domain of Cfap298 governs left-right symmetry breaking in vertebrates.Journal of cell science · 2025Article
- Prostaglandin E2 inhibits adipogenesis through the cilia-dependent activation of ROCK2.Journal of cell science · 2025Article
- Importin α regulates ciliogenesis and cilia length with implications for Xenopus nephrogenesis.Journal of cell science · 2025Article
- ARL13B-Cerulean rescues Arl13b-null mouse from embryonic lethality and reveals a role for ARL13B in spermatogenesis.Journal of cell science · 2025Article
- Platelet-derived growth factor signaling in porcine testicular tubular somatic cells.Cell and tissue research · 2025Article
- BBS8-dependent ciliary Hedgehog signaling governs cell fate in the white adipose tissue.The EMBO journal · 2025Article
- "Design principles of a membrane-spanning ubiquitin ligase".bioRxiv : the preprint server for biology · 2025Article
- ARL13B-Cerulean rescuesbioRxiv : the preprint server for biology · 2025Article
- RAB23 loss-of-function mutation causes context-dependent ciliopathy in Carpenter syndrome.PLoS genetics · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfill sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely available, and easy-to-use ImageJ plugins. CiliaQ allows high-throughput analysis of 2D and 3D, static or time-lapse images from fluorescence microscopy of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease.
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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.