2026/04/21 by Menno ter Huurne, Rustem Salmenov, Amit Mandoli · 1 voice
Biochemistry, Genetics and Molecular Biology · Engineering · #Cell Image Analysis Techniques #Microfluidic and Bio-sensing Technologies #Single-cell and spatial transcriptomics
paper · pdf · doi:10.64898/2026.04.16.717288
openalex publication_date 2026/04/21 · openalex created_date 2026/04/22 · openalex updated_date 2026/07/31
Abstract Flow cytometry is widely used for high-throughput single-cell analysis. However, its data analysis relies on either costly commercial software or programming-intensive open-source tools. To bridge this gap, we developed FlowWeb, a freely accessible, web-based platform that combines the flexibility of the R/Bioconductor ecosystem with an intuitive graphical user interface. FlowWeb enables integrated workflows for data handling, quality control, gating, visualization and statistical analysis within a unified environment. FlowWeb integrates raw data, metadata, and analytical state within synchronized Bioconductor structures, enabling coherent analysis and visualization workflows. FlowWeb supports both manual and automated data-driven gating workflows. To evaluate its performance, we applied FlowWeb to an in-house flow cytometry dataset and compared its automated cell cycle and gating workflows to established commercial tools. FlowWeb’s automated cell cycle workflow produced consistent and reproducible results across replicates and demonstrated high concordance with reference analyses, highlighting the platform’s robustness. FlowWeb’s advanced visualization tools include a wide range of fully customizable individual, overlay, and statistical plots. To enhance usability and reproducibility, the FlowWeb platform provides optional user-accounts that allow storage of reusable configurations, including quality control presets, gating definitions, and plot templates. By lowering technical barriers without compromising analytical rigor, FlowWeb facilitates accessible, reproducible, and scalable flow cytometry data analysis for a broad range of users in research and clinical settings.