Research workbench

Flow Cytometry Data Analysis Software

Free online flow cytometry FCS and FlowJo workspace analyzer. Interactive gating, FlowJo gate import, multi-file overlay, publication-grade plots. No upload, runs in browser.

Upload FCS Files

FCS 2.0FCS 3.0FCS 3.1ZIP

Drag & drop files or click to browse (FCS 2.0/3.0/3.1, any extension, max 50MB)

Multiple files supported

What this tool does

A browser-based flow cytometry analysis workspace. Upload FCS 2.0/3.0/3.1 files, import FlowJo workspace gates, apply compensation, draw polygon/rectangle/threshold/quadrant gates interactively, and export publication-quality scatter plots and overlay histograms.

Workflow

Upload — Drag and drop one or more FCS files.

Import Workspace — Optionally import matching rectangle / ellipse gates from a FlowJo .wsp file.

Compensate — Auto-detect spillover matrix from FCS metadata, or paste your own.

Gate — Draw polygon / rectangle / threshold / quadrant gates on scatter plots. Build hierarchical gating strategies with drill-down analysis.

Analyze — View per-population statistics (count, %, mean, median, CV) across all files and gates.

Export — Download SVG / PNG plots or CSV statistics tables. SVG includes gate overlays; axis scale and label are preserved.

Frequently Asked Questions

Is any data uploaded to a server?

No. All FCS parsing, gating, and statistics run entirely in your browser using Web Workers.

How many events can it handle?

Up to ~2 million events per file. Display uses intelligent downsampling (50K) for responsive interaction; full statistics are computed on all events.

What FCS versions are supported?

FCS 2.0, FCS 3.0, and FCS 3.1 with float, double, integer, or ASCII listmode data.

Can I import FlowJo workspace gates?

Yes. You can import matching gates from a FlowJo .wsp workspace for the active FCS file. Rectangle gates are imported directly, and ellipse-style gates are converted into polygon gates.

Can I compare multiple samples?

Yes. Load up to 10 files simultaneously. Overlay histograms show all files with line-style + color differentiation. Statistics table compares all files × all gates.