ArticleCilia2019
New software for automated cilia detection in cells (ACDC).
Article in Cilia, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 30 citations in OpenAlex.
- Cilia SubQ: a modular suite of semi- and fully automated pipelines for analysis of primary cilia and ciliary subdomains.Methods (San Diego, Calif.) · 2026Article
- Missense variants in KATNA1 alter microtubule dynamics and underlie dominant macular dystrophy.Research square · 2026Article
- Cilia SubQ, a modular suite of pipelines for automated analysis of primary cilia and ciliary subdomains.bioRxiv : the preprint server for biology · 2026Article
- Brain vascular stability relies on PAK2-cilia-PDGF-BB-HSPGs on basolateral side of endothelium.Life science alliance · 2026Article
- Analysis of Primary Cilium-Bearing Human Neuroprogenitors Using Flow Cytometry.Stem cells international · 2026Article
- New Insights into the Molecular Actions of Grosheimin, Costunolide, and α- and β-Cyclocostunolide on Primary Cilia Structure and Hedgehog Signaling.International journal of molecular sciences · 2025Article
- A 3D SVZonChip Model for In Vitro Mimicry of the Subventricular Zone Neural Stem Cell Niche.Bioengineering (Basel, Switzerland) · 2025Article
- A Novel Framework for Quantitative Analysis of Neuronal Primary Cilia in Brain Tissue.bioRxiv : the preprint server for biology · 2025Article
- CU Cilia - an application for image analysis by machine learning - reveals significance of cysteine cathepsin K activity for primary cilia of human thyroid epithelial cells.Frontiers in endocrinology · 2025Article
- Revealing Rotational Characteristics of the Uniflagellate Mutant ofmicroPublication biology · 2025Article
- detectCilia: An R Package for Automated Detection and Length Measurement of Primary Cilia.Bioinformatics and biology insights · 2024Article
- A Chemically Inducible Organelle Rerouting Assay to Probe Primary Cilium Assembly, Maintenance, and Disassembly in Cultured Cells.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Emerging principles of primary cilia dynamics in controlling tissue organization and function.The EMBO journal · 2023Review
- Ciliogenesis mechanisms mediated by PAK2-ARL13B signaling in brain endothelial cells is responsible for vascular stability.Biochemical pharmacology · 2022Article
- A protocol for generation and live-cell imaging analysis of primary cilia reporter cell lines.STAR protocols · 2022Article
- Fluorescence imaging of beta cell primary cilia.Frontiers in endocrinology · 2022Article
- Quantitative Determination of Primary Cilia Protein Distribution Using Immunofluorescence Staining and MATLAB Analysis.Bio-protocol · 2021Article
- Impaired Ciliary Beat Frequency and Ciliogenesis Alteration during Airway Epithelial Cell Differentiation in COPD.Diagnostics (Basel, Switzerland) · 2021Article
- Artificial Intelligence Approaches to Assessing Primary Cilia.Journal of visualized experiments : JoVE · 2021Article
- CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images.The European physical journal. E, Soft matter · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundPrimary cilia frequency and length are key metrics in studies of ciliogenesis and ciliopathies. Typically, quantitative cilia analysis is done manually, which is very time-consuming. While some open-source and commercial image analysis software applications can segment input data, they still require the user to optimize many parameters, suffer from user bias, and often lack rigorous performance quality assessment (e.g., false positives and false negatives). Further, optimal parameter combinations vary in detection accuracy depending on cilia reporter, cell type, and imaging modality. A good automated solution would analyze images quickly, robustly, and adaptably-across different experimental data sets-without significantly compromising the accuracy of manual analysis.
methodsTo solve this problem, we developed a new software for automated cilia detection in cells (ACDC). The software operates through four main steps: image importation, pre-processing, detection auto-optimization, and analysis. From a data set, a representative image with manually selected cilia (i.e., Ground Truth) is used for detection auto-optimization based on four parameters: signal-to-noise ratio, length, directional score, and intensity standard deviation. Millions of parameter combinations are automatically evaluated and optimized according to an accuracy 'F1' score, based on the amount of false positives and false negatives. Afterwards, the optimized parameter combination is used for automated detection and analysis of the entire data set.
resultsThe ACDC software accurately and adaptably detected nuclei and primary cilia across different cell types (NIH3T3, RPE1), cilia reporters (AcTub, Smo-GFP, Arl13b), and image magnifications (60×, 40×). We found that false-positive and false-negative rates for Arl13b-stained cilia were 1-6%, yielding high F1 scores of 0.96-0.97 (max. = 1.00). The software detected significant differences in mean cilia length between control and cytochalasin D-treated cell populations and could monitor dynamic changes in cilia length from movie recordings. Automated analysis offered up to a 96-fold speed enhancement compared to manual analysis, requiring around 5 s/image, or nearly 18,000 cilia analyzed/hour.
conclusionThe ACDC software is a solution for robust automated analysis of microscopic images of ciliated cells. The software is extremely adaptable, accurate, and offers immense time-savings compared to traditional manual analysis.
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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.