Data annotation by keywords post-processing allows for improved organization, ordering, and iteration within FlowJo.
Meta-data, information about the data, can be added to your FCS (Flow Cytometric Standard) files either at the time of collection using the acquisition software or post-acquisition in FlowJoTM. All cytometers will automatically set minimal information through the use of keywords, which are short strings of text added to the header of FCS files identified by letter codes. The list of keywords required by the FCS standard are available here. To add additional keywords either follow the instructions in your acquisition software or do it in FlowJo afterwards as described in this documentation.
To display any keywords that are already present in an FCS file loaded into FlowJoTM, simply press on the “Add keyword” icon and select 1 or multiple FCS keywords to be displayed in the sample area (Figure 1).
Figure 1. Adding FCS keywords to the sample display as columns (here Well ID and $DATE)
Adding New Keywords
To add a new keyword click on the Add Keyword icon in the context navigation bar (Figure 2.1). A keyword name is required and optionally a uniform value (Figure 2.2). Once a keyword is added, it can be shown within the keywords tab (Figure 2.3) or can be as well displayed in the sample table within the samples panel by using the Add keyword icon (Figure 2.4).
Figure 2: Adding New Keyword (here *Donor ID) with a unform value (here example Donor No.14)
Editing and Ordering Keywords
Newly added keywords, as well as FCS file derived keywords, can be edited under the Keyword tab. This allows the user to further process or modify keywords in FlowJoTM post-acquisition. Examples of some frequently used cases are modifying the fcs File Name or the Parameter Stain Name.
To change a keyword name or value simply double click on the Cell subject to make edits (Figure 3).
Figure 3. Editing an fcs file name from Tube1.fcs to FMO_control.fcs
Keywords displayed in the samples panel can be further used to organise sample, and order them alphabetically or numerically. To order the samples simply click on the upper or lower arrow for ascending or descending order respectively (Figure 4a,b).
(a) (b)
Figure 4. Ordering samples in the samples panel using numerical Keywords added post acquisition. a) ascending order based on "*Order Sort Keyword" values; b) descending order based on "*Order Sort Keyword" values