How gating works

A gate is the region of the FL1 × FL2 plot whose events count as cells. Everything a sample reports — TCC or ICC, HNA, LNA, HNAP and ACC — follows from its gate and the HNA split, so changing the gate changes the numbers. This page explains where gates come from and which one counts each sample. The procedures are in Edit a gate, Apply a gate to history and Hand-gate a sample.

Everyone can see which gate counted a sample. Only the Manager and Admin roles can change gating.

What a gate holds

The gate — a polygon of 3 to 1000 points on the FL1 × FL2 plot. Events inside it are counted: the total cell count (TCC) for TCC-D samples, the intact cell count (ICC) for ICC-A samples.
The HNA split — an FL1 value. Counted events above it are HNA, below it LNA.
An ACC region — optional: a second polygon for an additional cell count.

The gate library

Gates are kept per workspace in the gate library, Settings › Workspace Settings › Gates. Each library gate has a unique name, one measurement type (TCC-D or ICC-A) and a list of versions. A series can follow one library gate; several series can follow the same one.

Gates are not drawn in the library. A gate is always drawn on a real sample, in the gate editor, and saving it for the series either creates a gate or adds a version. The library is where you find, rename, inspect and archive them — see Manage the gate library.

Versions. Every save of changed geometry to a library gate adds a version. The newest version is the live one — the one new samples are counted with. Versions are never changed or deleted, because samples keep a reference to the version that counted them. To go back to an older shape, draw it again and save: that adds a new version.

Which gate counts a sample

Four sources can provide a sample’s gate. The first one that defines a region for the sample’s type wins:

Order	Source	Label on the sample	Where it comes from
1	Hand gate	Hand-gated	Drawn for this one sample in the gate editor.
2	Library gate	name vn	The gate the sample’s series follows, at the version that counted it.
3	Device gate	Device gate	The gating the instrument sent with the sample.
4	Default gate	Default gate	The platform’s fallback.

A series that follows no library gate is counted with whatever each instrument sends. Detaching a series from its gate (Clear gate) returns it to that.

What a recompute is

When a gate changes, samples already measured keep the numbers they were counted with — unless you ask for them to be counted again. Counting a sample again with the gate that now applies to it is a recompute (or regate). It happens:

at once, for the one sample, when you save a hand gate or put a sample back on its series’ gate;
in the background, for every sample of the series from a day you choose, when you save with This series, including history.

A recompute changes the cell counts, the HNA/LNA split and HNAP, the ACC value, and the gated cross-scatter plot and FL1 histogram.

A recompute keeps the FCS file, the FL1 × FL2 density plot of all events, and every earlier calculation: the previous numbers move into the sample’s Calculation history, where you can compare them with the new ones and see the gate each one ran under.

Hand-gated samples outrank everything

A hand gate is a judgment about one sample — an unusual measurement that the series’ gate counts wrongly. It wins over every other source and it stays: history recomputes skip hand-gated samples, and the scope step tells you how many it will leave alone. Nothing but Use the series’ gate puts a hand-gated sample back on its series.