Histograms display a frequency distribution of the data, as a function of fluorescence intensity. The histograms can be smoothed (by default) or unsmoothed; this option has little effect when more than a few thousand events are in the gate. Shown below are the same dataset shown with and without smoothing turned on. (Right click, select Options > Smoothing)

The Y-axis for histograms is the number of cells falling within each "bin" of the histogram; there are 256 bins for each histogram.

You can manually set the lower and upper limits on the Y axis; the default is to have FlowJo determine the optimal limits. To set these limits, use the Graph Specifications Dialog, by opening the Options triangle in the graph window.

You can export data from the graph window in various forms.

1. From the Edit menu you may choose Copy Picture to place a bitmap copy of the graph without gates on the clipboard.
2. Copy Picture with Gates will include any gates you have drawn.
3. Copy Histogram as Text will place the histogram data (channel numbers & channel counts) on theclipboard. You can paste to a text editor or straight into a spreadsheet. When you paste them into a spreadsheet, you will create the two new columns of the histogram data. (Note: a few graphics programs will preferentially paste a text item (the column data) instead of a graphic item from the clipboard. If you encounter this problem, Copy Picture so that FlowJo only copies the graphic item onto the clipboard.)

4. Copy Statistics will place on the clipboard any statistics you have created by selecting the Statistics disclosure triange at the bottom of the graph window (right.)
5. Copy Gate together with Paste Gate allow you to copy a gate from one graph to another either by opening another graph window from the Workspace or by using the arrows at the upper right corner of the Graph window to move to the next population in the Workspace list.
6. Copy to Layout Editor Lets you paste the graph and any gates into the layout editor as if dragged from the Workspace.
7. Add Statistic duplicates the behavior of the Add Statistic button at the bottom of the window.

See also the page on CDF displays.