ArticleCytometry. Part A : the journal of the International Society for Analytical Cytology2016
flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data.
Article in Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Guidelines for Gating Flow Cytometry Data for Immunological Assays.Methods in molecular biology (Clifton, N.J.) · 2027Article
- MAP Crosslinker Chirality Regulates Macrophage Polarization Through MD-2 Engagement and Enables Tunable Immunomodulation Through Novel Peptide Design.Advanced healthcare materials · 2026Article
- Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources.International journal of molecular sciences · 2026Review
- A Subset of Pro-inflammatory CXCL10+ LILRB2+ Macrophages Derives From Recipient Monocytes and Drives Renal Allograft Rejection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Development and computational analysis of high dimensional spectral flow cytometry data for the resolution of innate lymphoid cells in the mammary tumor microenvironment.Frontiers in immunology · 2026Article
- Quantification of EV-associated miRNA in liquid biopsies for biomarker signature development.Extracellular vesicles and circulating nucleic acids · 2026Review
- L-Phenylalanine is a metabolic checkpoint of human Th2 cells.Cell reports. Medicine · 2025Article
- Assessment of Biocontainment Efficacy and Flow Cytometric Impact of a Novel Platform in High Containment Laboratories.Applied biosafety : journal of the American Biological Safety Association · 2025Article
- Application of Artificial Intelligence in Inborn Errors of Immunity Identification and Management: Past, Present, and Future-A Systematic Review.Journal of clinical medicine · 2025Review
- Beyond the Limits: How Is Spectral Flow Cytometry Reshaping the Clinical Landscape and What Is Coming Next?Cells · 2025Review
- Automated cytometric gating with human-level performance using bivariate segmentation.Nature communications · 2025Article
- Machine Learning Methods in Clinical Flow Cytometry.Cancers · 2025Review
- Dysregulated NK cell activation and myeloid-lymphoid imbalance underpin COPD progression: insights from high-dimensional immune profiling and smoking-induced immune remodeling.Frontiers in immunology · 2025Article
- Comparison of three machine learning algorithms for classification of B-cell neoplasms using clinical flow cytometry data.Cytometry. Part B, Clinical cytometry · 2024Article
- CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data.BMC bioinformatics · 2024Article
- FlowAtlas: an interactive tool for high-dimensional immunophenotyping analysis bridging FlowJo with computational tools in Julia.Frontiers in immunology · 2024Article
- CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data.Nature communications · 2023Article
- Computational Methods for Single-Cell Proteomics.Annual review of biomedical data science · 2023Review
- Flow Cytometry: The Next Revolution.Cells · 2023Review
- Immunogenicity of poxvirus-based vaccines against Nipah virus.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Modern flow cytometry systems can be coupled to plate readers for high-throughput acquisition. These systems allow hundreds of samples to be analyzed in a single day. Quality control of the data remains challenging, however, and is further complicated when a large number of parameters is measured in an experiment. Our examination of 29,228 publicly available FCS files from laboratories worldwide indicates 13.7% have a fluorescence anomaly. In particular, fluorescence measurements for a sample over the collection time may not remain stable due to fluctuations in fluid dynamics; the impact of instabilities may differ between samples and among parameters. Therefore, we hypothesized that tracking cell populations (which represent a summary of all parameters) in centered log ratio space would provide a sensitive and consistent method of quality control. Here, we present flowClean, an algorithm to track subset frequency changes within a sample during acquisition, and flag time periods with fluorescence perturbations leading to the emergence of false populations. Aberrant time periods are reported as a new parameter and added to a revised data file, allowing users to easily review and exclude those events from further analysis. We apply this method to proof-of-concept datasets and also to a subset of data from a recent vaccine trial. The algorithm flags events that are suspicious by visual inspection, as well as those showing more subtle effects that might not be consistently flagged by investigators reviewing the data manually, and out-performs the current state-of-the-art. flowClean is available as an R package on Bioconductor, as a module on the free-to-use GenePattern web server, and as a plugin for FlowJo X. © 2016 International Society for Advancement of Cytometry.
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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.