Why can’t I change my plot axis labels from the Name keyword to the Stain keyword?

A common problem when displaying plots with flow cytometry data is to display correct text in the axis titles. Depending on the instrument, and the settings that were used during acquisition, the information might be stored in the Name keyword of the parameter in FCS file, or the Stain keyword.

In version 3, it was possible to change each plot individually – in the axis options formatting category, you had the ability to change from Name to Stain, or even Name + Stain, or Stain + Name.

In FCS Express 5 and greater (and in FCS Express 4), you can still make that change, but you only need to make it once – before the plot is inserted. You can do this by clicking on the File tab and Options command. Then, click on Data Loading and select the FCS Files Option category.  Change the value of Keyword to Use as Parameter Name and click OK.

You can read more information about setting up axes labels in our manual:

• FCS File Options
• Axes formatting
• Parameter Label Sets

NOTE: Once the user option is changed, it will only apply to newly loaded .fcs file data or new layouts. To have your existing plots reflect the new Parameter Name please follow the steps below:

1. Make changes to your Parameter Name preferences as mentioned above.
2. Save the layout with “No Link” by selecting the File tab>Save Layout As>Save Layout As. Choose the radio button on the right under Data Files for No Link.
3. Click Save.
4. Close the Layout.
5. Open the Layout.
6. Reload your data into the plots via the Data List.
7. Save your layout as you normally would do.

The new Parameter Name preference will now be in place and the changes will not have to made again.

A tutorial with step-by-step instructions for changing Axis Labels and other commonly edited FCS Express User Options is also available.