Getting Started
Welcome to Cytomaton
Cytomaton is an AI-first cloud platform for flow cytometry data analysis. It runs entirely in your web browser — no desktop software to install. Upload your FCS files, draw a few gates, and the AI learns your gating style to suggest boundaries for new samples automatically.
The interface has three main areas: an experiment workspace (file list, scatter plots, gating tree), an AI chat panel (domain-expert assistant), and analysis tools (FlowSOM, UMAP/tSNE, heatmaps).
Create an experiment
From the Dashboard, click New Experiment. Give it a name that matches your experiment (e.g., "PBMC CD4/CD8 panel 2026-03-09").
You can also upload files without creating an experiment first and organize them later.
Upload FCS files
Drag and drop your .fcs files into the upload zone. Cytomaton supports FCS 2.0, 3.0, and 3.1 from BD FACSDiva, Cytek Aurora, Beckman CytoFLEX, and Sony instruments. Each file shows a per-file progress bar during upload.
Spectral data? Cytomaton auto-detects spectral files and prompts you to set up unmixing before gating.
Maximum file size: 2 GB per FCS file, up to 10M events per file.
Draw your first gate
Select a file in the sidebar. The scatter plot loads automatically with FSC-A vs SSC-A as the default view. Use the toolbar or keyboard shortcuts to draw gates:
| Shortcut | Gate type |
|---|---|
| R | Rectangle gate |
| P | Polygon gate |
| E | Ellipse gate |
| Q | Quadrant gate |
| Delete | Remove selected gate |
| Ctrl+Z | Undo last vertex |
| ? | Show all shortcuts |
Check your statistics
The Gating Tree panel on the right shows live-updating statistics for each population: % of parent, % of all events, and event count. Statistics update in under 100 ms.
MFI values are available for spectral data with parameter pinning (top 5 parameters by default).
Export your results
Click the Export button in the toolbar to download publication-quality figures (PNG 300 DPI, SVG, PDF) or statistics as CSV.
For GraphPad Prism, use the Prism Export option — Column, Grouped, or XY layouts. PowerPoint export generates 16:9 slides with marker labels and scales.
MIFlowCyt metadata export is available for NIH DMS Policy compliance.