How do I adjust the axes to display small particle data from Amnis CellStream?

Small particle data from Amnis CellStream might require the user to customize the axis setting (mainly the Resolution Minimum and the Resolution Maximum) to better display the data in plots. This can be done specifically on a single (few) plots or, more broadly, by creating an Instrument Specific Settings rule for CellStream.

Adjust axes on specific plot(s)

After selecting the plot(s) of interest

1. Be sure that the Range on both axes is set to Automatic (this is done from the Formatting Axis dialog).

2. Change the Resolution Minimum and the Resolution Maximum in the Plot Specific Options so that the Min/Max are appropriate for your data. This should be done for both the X and Y axes.

Note: change the resolution on a plot before creating any gate on it. When the resolution is changed, and gates are already on the plot, gates should be recreated. This is very important to ensure that statistics are properly calculated. To recreate a gate, simply draw a new gate on the plot of interest and the select to “Replace an existing gate”.

Creating an Instrument Specific Settings rule for CelllStream

The procedure below creates a rule that will automatically scale scatter parameters for CellStream data with the preferred Min/Max Axis value. If all data require these Min/Max values, as default, these would not have to be changed plot by plot.

1. Create a new rule in the instrument-specific settings in your User Options. Please refer to this page for more details.

This rule will be applied to new files. If there is data already in a layout:

2. Use the Refresh button in the Data tab (in the ribbon bar)

3. Recreate the gates on the plot displaying scatter parameters. This is very important to ensure that statistics are properly calculated. To recreate a gate, simply draw a new gate on the plot of interest and then select Replace an existing gate. See the screenshot below.

In FCS Express, you can replace an existing gate. The new gate will replace the old gate and the gating hierarchy and any link stats update automatically.