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Tools / Image analysis / Flow Cytometry Analysis
Image analysis

Flow Cytometry Analysis

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.

Gate flow cytometry data and read population fractions

Upload FCS files
FCS 2.0FCS 3.0FCS 3.1ZIP
FCS 2.0, 3.0, 3.1 (any file extension) or .zip · up to 50 MB
Multiple files supported

Synthetic sample for trying the workflow: lymphocytes (85%) and a low-FSC, high-SSC population (15%) on FSC/SSC

Guide and FAQ

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/ellipse/threshold/quadrant gates interactively, compare samples side by side, and export publication-quality scatter plots and overlay histograms. Your session is kept in the browser and can be saved to a file.

Workflow

  1. Upload — Drag and drop one or more FCS files.
  2. Import Workspace — Optionally import matching rectangle / ellipse gates from a FlowJo .wsp file.
  3. Compensate — Auto-detect spillover matrix from FCS metadata, or paste your own.
  4. Gate — Draw polygon / rectangle / threshold / quadrant gates on scatter plots. Build hierarchical gating strategies with drill-down analysis.
  5. Analyze — View per-population statistics (count, %, mean, median, CV) across all files and gates.
  6. Export — Pick what the figure includes (width, background, title, axes, grid, gates, percent labels, legend), then download SVG / PNG or print to a vector PDF. CSV covers statistics and per-event data.
  7. Save — The browser keeps your gates, compensation and layout and offers to restore them next time. Download a workspace file to reopen the session later, with or without the event data bundled in.

For membrane spot quantification with standard curves and background correction, see the in-browser Dot Blot analyzer.

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. Grid by sample gives each file its own panel on shared axes, overlay histograms differentiate files by line style and colour, and the statistics table compares all files × all gates.

Is my work saved if I close the tab?

Your gates, compensation and layout are saved in your browser as you work, and the tool offers to restore them next time. You can also download a workspace file — a small one with just the analysis settings, or a bundled one carrying the event data so the session reopens with no files on hand.

Can a gate apply to only one sample?

Yes. Any gate can be scoped to the active sample from the gate hierarchy and released back to all samples. Child gates follow their parent, since a child population is carved out of it.

How do I get a PDF figure?

Export PDF opens your browser's print dialog — choose "Save as PDF". The output is vector, and labels are typeset by the browser, so non-Latin text stays intact.

Version history

Version history for all tools is listed in the Chronicle.

View tool updates