FlowJo examines all data files in your workspace to build a list of the different staining panels. These are shown in the list box in the middle.  If you wish, you can select one or more of these to define that only samples stained with the particular combination of reagents should be added to the group.

You can also specify one or more criteria based on FCS keyword values.  Select an FCS keyword, a comparison, and the value to compare against; FlowJo will add samples only if they meet the selected criteria.

Finally, you can specify that the group take its samples only from another group (or to use all samples in another group)--essentially providing you with the ability to make subgroups.  Note that samples must fit all criteria specified in this window in order to be added to the group.

Note that you may manually add samples to a group by dragging and dropping them in the workspace window.  They will automatically become members of the group irrespective of the criteria you have established for the group.  As well, you may remove samples from a group by selecting them and deleting them (they will not be deleted from the workspace as long as they are members of the "All Samples" group).

If you choose to make a group "live", then FlowJo will examine any new data files that you read into the workspace to see if they fit the criteria for this group.  If they do, then they are automatically added to the group, and any group-based analyses are added as well.  If you are constructing "template" workspaces for future use by yourself or others, make sure that your groups are "live".

The color and style apply not only to the nodes of the group in the group list window, but also to any node in the samples which was created by the group AND is still identical to the group's version of the gate. This is how you can tell if a gate has been modified from the group's version: it will not appear in the same color/style as the group's version, but rather in black and plain text. Therefore, you should avoid having group nodes be shown in black with plain text: then you would be unable to distinguish gates which belong to the sample, and gates which belong to the group.

You can later change the name, style, and color of a group. However, the criteria used to add samples to the group apply only at the time that you create the group. In other words, if you later add more samples to the workspace, they will not be added to existing groups automatically.

If you want to create more than one group, click on the "Create" button; when you are making the last group, click on the "Done" button.