The interface
The file list
Section titled “The file list”Left side. Every open file, with the active one highlighted.
- Ctrl+Click to multi-select — the basis of batch analysis.
- Double-click a file to rename it. The name is a label in the workspace, not the file on disk.
Below the list, the file info bar shows the active file’s event count and key acquisition facts.
Metadata and parameters
Section titled “Metadata and parameters”Every FCS keyword is inspectable rather than hidden — useful when you need to know what the acquisition software actually recorded, and the first place to look when a channel is not what you expected.
The parameter editor lets you correct how a channel is labelled for the analysis.
Detector names and marker names disagree constantly in real files, and a channel
labelled FL4-A with no marker will not be understood by AI-1 —
naming it is what makes the panel readable.
The plot
Section titled “The plot”Centre. One plot, or a grid of them.
- Scroll to zoom.
- Click and drag to pan, in navigate mode.
- Double-click empty space to reset the zoom.
- Click an axis label to change the parameter and its scale.
The breadcrumb
Section titled “The breadcrumb”Directly above the plot, and easy to overlook. It shows which population you are currently inside after drilling into a gate.
This is the answer to “percent of what?”. If a number surprises you, look at the breadcrumb first.
The gating toolbar and gate list
Section titled “The gating toolbar and gate list”The toolbar selects the gate tool; the list shows the hierarchy with each population’s statistics, colour, and nesting.
Gates in the list are colour-coded, and the same colour identifies the population in plots and exports. See Gating.
Statistics
Section titled “Statistics”Counts, frequencies and per-channel statistics for every population, updating as gates change. There is also a correlation heatmap across parameters. See Statistics.
The AI panels
Section titled “The AI panels”Several, and they are not interchangeable:
| Panel | What it is |
|---|---|
| AI gating | AI-1 — our own model, on-device, fixed population list, abstains |
| Copilot | The LLM assistant — plans strategies, drives the app, propose-and-approve |
| Competence report | AI-1’s own account of what it can and cannot identify in this file |
| Gate review | A second look at gates you have already drawn |
| Data check | Acquisition and quality problems worth knowing before you interpret anything |
| Report | A written summary of the analysis |
| Batch insights | Patterns across a batch rather than within one file |
| Tutor / Quiz | Flow cytometry teaching, not analysis of your data |
The command palette
Section titled “The command palette”Ctrl+K. Fastest route to anything you can name. Worth learning early if you prefer keyboard to menus.
Preferences and theme
Section titled “Preferences and theme”Light and dark themes are both supported. Dark is worth trying for flow work specifically: sparse and rare-event populations read far more clearly as cyan on navy than as faint blue on white. That is legibility, not decoration.
Keyboard shortcuts
Section titled “Keyboard shortcuts”? at any time. Full list at Keyboard shortcuts.