The FlowJo workspace adorns samples with new icons, presented in three columns – known as badges.

1) The left-most column of badges showing the blue diamonds, indicates which samples have been viewed
  1. An empty diamond indicates the sample has not been viewed yet
  2. A blue diamond indicates the sample you are currently viewing in the graph window
  3. A blue diamond with a blue ring indicates a sample that has already been opened, but is not being viewed
2) The middle column indicates the state of the samples Quality Check result.
  • FlowJo will scan parameters vs Time looking for drifts in the signal. If a sample has problems this badge will be used to indicate the problem and its severity.
3) Lastly the right-most badge reflects the sample’s compensation status.
  • An empty box indicates that there is no compensation matrix applied to the data

    • this excludes fcs2.0 data where no matrix element is present to “tell” FlowJo if the data has been compensated or not
  • A gray grid on white background is given to samples compensated with the Acquisition matrix
    • The acquisition matrix is automatically applied to fcs3.0 data files upon load
  • A user-defined color is assigned to user-created matrices.

Double click the matrix to open the matrix editor.