Flow cytometry · research beta

SideScatter

Flow cytometry analysis in the browser. FCS parsing, compensation, transforms, gate masks with population ancestry, statistics and exports, all from one core.

Open SideScatter SideScatter, formerly Gatecraft, is served from gatecraft.bio while the rename completes.

What it does

• Opens FCS files and FlowJo .wsp workspaces and applies the gates to matching FCS files.
• Compensation, transforms and a gate tree that records each population's ancestry.
• Statistics with the test, n and correction shown next to the number they describe.
• Tested against real CytoTrol FCS files in the automated test suite.

How close is workspace import

An internal comparison, not an external benchmark: on one 13-colour workspace, SideScatter's gating reproduced 775 of 898 FlowJo stored counts within 1 percent. The remaining differences were 1 to 7 percent, on small quadrant populations. There is no external reference implementation for this comparison yet, so check counts that matter against your own analysis.

Where your data goes

FCS event data stays in this browser. An AI request sends gate and channel names, counts and statistics shown on screen, never event data. A problem report you choose to send goes to the hosting provider's logs. A workspace share link carries the gating strategy in the link itself, without events. An AI key you choose to remember on this device is kept in unencrypted browser storage, so leave that option off on shared computers.

AI and connectors

The assistant is optional. Use your own key, or the limited hosted mode, which uses free models with low daily limits and is not for work you depend on. A local MCP connector is in development. See Connect your AI.

Limits

• The Jupyter notebook export is not yet recommended for analysis you need to repeat; it is being reworked and tested against a golden dataset.
• Results are not claimed to match FlowJo or openCyto numerically.
• Advanced functional research beta: features may change and there is no service level agreement.