Cytometry: FCS file analysis with assisted gating

2026.10.20-cytometrie-gating-assiste · 2026-10-20

Delivered build : d551d19c17c3f3b3af966f67af00e600d9e9cf20

Changes

New "Cytometry" entry in the Research group: an analysis groups FCS files (one tube = one file), like a usual cytometry workspace.
FCS 3.1 event reading, compensation with the file's own matrix (shown in the application), Logicle, biexponential, linear or log axis transforms.
Gates drawn with the mouse: rectangle, polygon, ellipse, interval, quadrant and boolean, in a hierarchy, with counts, percentages of parent and total, and median and mean per parameter. CSV export of the statistics.
Apply the selected gates to all tubes: button or Ctrl or ⌘ + Shift + A shortcut (Alt + Shift + A as a fallback). Copies are marked "not reviewed" and their statistics "provisional" until each tube's graph has been seen and the gate validated.
Each gate is validated on the displayed graph. The validation is tied to a fingerprint of that graph: any change to the gate or to the displayed data voids it, along with that of its child gates.
Otto and MCP: Otto describes each graph with numbers (percentiles, density valley, peaks), proposes gates from marker names (for example CD3+ for T cells) and refines the boundary deterministically. MCP tools are read-only.
Presets: a validated strategy is saved as a team template (markers and search logic, not coordinates) and applied to another tube.

Conventional cytometry only (10 to 20 parameters); no tSNE, UMAP, FlowSOM or spectral cytometry.
FCS files over 100 MiB are refused with a clear message.
Medians have not been compared with reference values; counts of rectangular gates were compared on real data (at most 0.07 point apart). Ellipse gates imported from an external workspace are not converted exactly.
A validation made by Otto does not prove the graph was seen; validation through the interface remains the reference.
Presets cannot yet be renamed or deleted. The keyboard shortcut has not been tried in every browser.