Flow cytometry
From FCS files to reviewed populations, statistics, and figures.
A flow workspace keeps your event data, sample annotations, gates, and analysis settings together. Use the workbench for interactive gating and the analysis consoles for population comparisons, statistics, and high-dimensional exploration.
Start with your data
- Sign in with Google, then choose Flow cytometry in the header.
- Create or open a workspace and upload your FCS files. Check the sample names, event counts, and channels.
- Open a sample in the gating workbench. Review compensation and transforms before building a gate hierarchy.
- Inspect the populations, save the analysis, and use the statistics or comparison tools for your experimental question.
To explore the controls first, open the synthetic demo in the gating workbench. Demo plots are not results from your own samples.
Workflow guides
Import files and organize samples
Import FCS and tabular event data, organize samples, and check channel metadata.
Build and review gates
Set up a gating strategy, choose axes and transforms, and review populations across samples.
Compensation and transforms
Inspect spillover matrices, compare corrected signals, and set channel display transforms.
Import a FlowJo workspace
Bring in a .wsp file, review the import report, and verify gates against the original samples.
High-dimensional analysis
Explore marker expression with embeddings and clustering, then review the resulting populations.
Use the AI agent and review results
Make specific analysis requests, inspect the agent’s actions, and prepare population statistics and figures.
Choose the right workspace
Use the flow workspace for individual events in FCS files. If you already have an exported table, use the Flow summary assay workflow with explicit sample, population, event_count, and parent_count columns; median_fluorescence is optional. That workflow computes population frequency as event count divided by parent count. It does not reopen raw FCS events, compensate channels, transform values, or reconstruct gates.
The header keeps Assays, Flow cytometry, and Docs in the same place. Open the menu beside Flow cytometry for its analysis tools. Profile, account settings, and flow preferences are in the account menu on the right.
AI usage
The free plan includes 20 free runs per calendar month (UTC), shared between assay and Flow analysis. Required setup answers are included with each run; later refinements and follow-up messages count as another run. Manual gating, compensation, and plotting do not use runs. See Pricing for plan details.