Question 1

Is there a free alternative to FlowJo?

Accepted Answer

Yes. Cytomaton is a free, browser-based flow cytometry analysis platform with AI-assisted gating, compensation, spectral unmixing, and publication-ready export. It imports FlowJo .wsp workspaces and exports to GraphPad Prism format.

Question 2

What is the best free flow cytometry analysis software?

Accepted Answer

Cytomaton offers cloud-native flow cytometry analysis with AI that learns your gating style, FlowSOM clustering, UMAP/tSNE dimensionality reduction, automated data QC, and cell cycle analysis — all free in your browser with no software to install.

Question 3

Can I analyze FCS files online?

Accepted Answer

Yes. Cytomaton supports FCS 2.0, 3.0, and 3.1 files from any cytometer brand (BD FACSDiva, Cytek Aurora, Beckman CytoFLEX, Sony). Upload files via drag-and-drop, gate interactively, and export publication-ready figures — entirely in the browser.

Question 4

What compensation matrix tools are available for flow cytometry?

Accepted Answer

Cytomaton builds compensation matrices from single-color controls with before/after validation, over-compensation detection, and per-fluorochrome threshold override. It also supports full spectral unmixing for Cytek Aurora and Sony ID7000 data.

Documentation

Getting Started

Gating & Analysis

AI Features

Data Import & Export

Collaboration & Sharing

Keyboard Shortcuts