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Flow Files and Templates

Multi-file workflows, reusable gating templates, file concatenation, sub-groups, and quality control.

Templates

Save a gating strategy once and apply it to new files later.

Saving a Template

Once your gating hierarchy is in place, click Save as Template in the sidebar. Name it and give it a description. The template captures your gates, plot layout, and compensation matrix.

Applying a Template

Open a new analysis or load a new file and click Apply Template. Pick from your saved templates and decide whether to:

  • Replace the existing gates with the template's
  • Add the template's gates alongside what's already there

The template's parameter names are matched against the new file's channels automatically, so renamed or differently-ordered channels still line up correctly.

Multi-File Analysis

Load multiple FCS files into a single analysis to compare across samples. The Files panel in the sidebar lists every loaded file. Pick the working set by checking the files you want active:

  • One file checked: standard single-file mode
  • Multiple files checked: comparison mode, where you can flip between files in the navigation bar above the plots
  • Aggregate statistics across the whole working set are available from the bottom panel

Shift + Left/Right cycles through files quickly without leaving the plot.

Sub-Groups

For panels of files that fall into natural groups (treatment vs control, donor A vs B vs C, timepoint 0 vs 24 vs 48), define sub-groups in the Files panel. Drag files into a sub-group, name it, and use it later for:

  • Banded aggregate statistics (each sub-group shown together)
  • Faceted overlay comparisons
  • Quick selection of the whole sub-group as your working set

Concatenating Files

When you have multiple files loaded, click Concatenate Files in the sidebar to merge them into a single virtual file. Useful for:

  • Combining technical replicates
  • Pooling controls to establish more robust gating boundaries
  • Treating data from multi-tube panels as one dataset

The concatenation dialog box shows files with checkboxes, event counts, and parameter alignment. Enable Add source file parameter (on by default) to add a channel that tags each event with the file it came from, so you don't lose provenance after concatenation.

Quality Control

Open the Quality Control dialog box from the Cell Analysis section in the sidebar. QC runs kinetics detection across every fluorescence parameter at once to surface acquisition artifacts: clogs, bubbles, flow-rate changes, signal drift.

QC presents:

  • An overall stability score
  • A grid of mini time-series plots with anomalous bins highlighted
  • Suggested exclusion regions with checkboxes

Adjust the number of time bins and the anomaly threshold to tune sensitivity. When you apply the selected exclusion regions, events from those time periods are filtered out of every plot in the workspace, not just the time histogram. A green dot next to the Quality Control button indicates the filter is active.

Reopen QC at any time to review which time regions are excluded. Use Remove to clear the filter entirely.

Next Steps

Flow advanced analysisFlow reporting