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Exporting Populations

After you’ve gated populations, you can export events as FCS or TSV files, or create a new experiment containing your gated populations.


  1. Click export populations in the left sidebar.
  2. Select the populations to export in the Populations selector.
  3. Select the FCS files to export from in the FCS Files selector. One output file will be generated for each combination of population and FCS file.
  4. Select the output file format (FCS, TSV with header or TSV without header).
  5. Select the compensation to use.
  6. Select if you want the output data to be compensated or not. See Export Compensated Data below.
  7. To download a ZIP file, click download. To export the populations to a new experiment, click export to new experiment.


It’s best to download large files with a stable internet connection, such as a fast ethernet connection or strong wifi signal.

Export Compensated Data

For TSV format, this setting writes the compensated values into the exported file. The channel names in the header row will be bracketed to indicate that they are compensated (e.g. <PE-A (CD3)>).

For FCS format, this setting writes the selected compensation matrix into the exported file’s $SPILLOVER header keyword without changing the numerical values in the file body. That is, it makes the selected compensation the new “file-internal” compensation.


Subsampling pseudo-randomly selects a subset of events from your files, either before or after gating.

Applying subsampling before gating lets you equalize the number of events in each file. While this can possibly enable you to make absolute numerical comparisons of the number of cells in populations between files, you must be certain that your samples are otherwise comparable. For example, if one sample contained 50 percent debris and another contained only 10 percent debris, then you cannot make absolute numerical comparisons of non-debris cells.

Applying subsampling after gating lets you look at a fixed number of a cell type of interest—for example, look at 500 dendritic cells.

You can either subsample up to an absolute number, or to a percentage.

Optionally, you can specify a seed for the random number generator. Using the same seed and subsampling parameters will yield the same set of subsampled events every time. Use this for deterministic (reproducible) subsampling.

Add Event Number

Selecting this option adds an “eventNumber” column to the FCS or TSV file(s), containing the 0-based index of each event in the original (ungated) FCS file.

Filename Template

By default, exported TSV/FCS files are named with the source file’s filename and the population name. You can specify a custom template to use instead, comprised of any combination of the source file’s filename, ID and annotation values, and the population’s name and ID, along with any other fixed characters. (Characters that are unsafe for use in filenames will be removed upon export.) To insert a new template token, type the { character into the filename template field and select the desired token from the dropdown list.