Free, open-source flow cytometry analysis workbench for conventional, spectral and mass cytometry. Gating, compensation, spectral unmixing, QC, clustering/UMAP, statistics and publication figures. Rea
CytoWeave is a flow cytometry analysis workbench for conventional, spectral and mass cytometry. It runs on your own computer as one self-contained program: a single command installs it, and it needs no license server, account, Python, R or plugins. Files are read and analyzed in your browser and never leave your machine.
It covers the analysis loop a cytometry lab works through every day, and checks each step:
- gating many samples consistently, with per-sample adjustments, and gates adapted to each sample with a confidence for each; - spillover from single-stain controls, checked against those controls; - spectral unmixing with autofluorescence, and a comparison of how the choice of unmixing model changes the result; - panel design: a panel's spread predicted from the instrument's own noise before the panel is run; - acquisition QC that finds clogs and bubbles and leaves clean data alone, also as the instrument writes each file; - the instrument itself: detector efficiency Q and background B from beads, Levey–Jennings charts across runs, and a library of reference spectra; - batch normalization and debarcoding; - clustering and UMAP/t-SNE maps that report how far they can be trusted; - statistics tables and group comparisons with the right test for the design, and a check of whether a conclusion survives other reasonable analysis choices; - samples compared with a control (SED, Overton, probability binning), and rare populations reported with exact intervals and detection limits; - formula channels (ratios and other expressions of channels), fluorescence in calibrated ME
From the project README.
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