Getting started with FCS analysis

1. Open your data

Choose Try the demo dataset to explore the workspace, or open FCS files from your computer. The demo uses example data and does not require you to prepare files first.

2. Review samples and channels

Select a sample to inspect its dot plot. Choose the channels shown on the axes, review event counts, and check whether the file contains compensation information. Available controls and parameters depend on the FCS file.

3. Define populations

Create gates on the plots and arrange populations in a gating tree. Use groups to compare related samples and review overlays or summaries. Confirm gates against the plots and experimental context before interpreting results.

4. Review and export a report

Open Report to review the report content, select its language and format, then export. Read the report preparation guide for an overview.

Data handling

FlowApp is designed for local-first browser use. Your selected files are opened by the browser workspace. Before using any optional AI service or sharing exported results, review the applicable settings and your organization's data policy.

Troubleshooting

• Confirm the file is a valid FCS file and try opening it again.
• Large files may take longer to read and draw.
• If a plot looks stale after an update, reload the page.
• For help, visit Contact.