Batch and specialised analysis

Requires a license.

Batch analysis

The point of batch analysis is that a gating strategy is a decision you should make once and apply consistently — not re-draw per sample, where it drifts.

1. Build and check the strategy on one representative sample.
2. Ctrl+Click to select the files it should apply to in the file list.
3. Run the batch.
4. Read the results as one table, a row per sample.

Check a few samples individually afterwards. A strategy that fits the sample you built it on can fail on a sample with different staining intensity or a shifted population, and a batch table looks equally confident either way. Spot-checking the outliers is the whole discipline here.

Dose-response

For experiments where samples are a concentration series: extract a population frequency or channel statistic per dose and fit the response.

Proliferation analysis

For dye-dilution proliferation experiments — CFSE and similar — where successive generations appear as halving peaks in a single channel.

Graph builder

For plots the standard views do not cover — arranging populations and statistics into the figure you actually want rather than the one the layout offers.

Practical sequence for an experiment

1. Open every file in the experiment.
2. Fix channel names once — see the parameter editor in The interface.
3. Compensate, from controls where you have them.
4. Build the strategy on one representative sample, and check it.
5. Batch it across the rest.
6. Spot-check the outliers by hand.
7. Export statistics, the compensation matrix, and the workspace.