As of FlowJo (10.0.7), there is a tool to assist in rapid visualization of plate-based flow data.

Looking for outliers in a flow cytometry-based assay?  There is a new plate tool built into the layout.

In the example below, I would like to generate heatmaps for the MFI (median fluorescence intensity) of phosphorylated STAT5 on CD4+ cells.

In order to do this:

    • Open the Layout Editor.  
    • Select the plate tool and put it into the layout to set a single well.
FlowJo Layouts---20130618
  • By default, there is only one cell.
  • Select the group from which the statistics will be drawn using the plate menu at left. In this case, I have selected the group – “Plate 1.”
  • Drag and drop the statistic you would like heatmapped onto the plate.
  • The plate will rescale and display the heatmap of the statistic:

Screen Shot 2013-06-18 at 10.33.07 AM-1

Heatmap of pSTAT5 MFI in CD4+ T cells.

  • At right you’ll note that the statistic in the heatmap for this plate has been updated as well as annotation at the bottom left of the plate.  In addition, there is an option to display the sample name at right.

Additional Options:

If you drag a second statistic into the plate, you can generate a split heatmap of both statistics:


The tray at the right will allow you to control which statistic is listed in which halve:

FlowJo_Layouts---20130814 2


Finally, up to 10 statistics can be viewed using Chernoff faces:

FlowJo_Layouts---20130814 3

The list of attributes that can be assigned is presented here:

FlowJo_Layouts---20130814 4



We are also working on methods of plate annotation to facilitate automated analysis, and encourage you to contact us (flowjo [at] or visit our information page for high throughput analyses) to get the latest update to this platform.


See Also: