Define Matrix...

Brings up the Compensation Dialog Window to begin the process of defining a new compensation matrix. To use this menu item, you must have a sample selected from the workspace window: this is how FlowJo knows which fluorescence channels are available.

Load Matrix...

Asks you to open up a previously-created and saved compensation matrix file and load it into the workspace. To save a matrix file from another workspace, use the Edit/Save matrix option.

Define Transformation...

If a lot of cells are squished against the axis after compensation, you can change the display. This allow a more intuitive display of the data by changing the scale of the graphs using Bi-Exponential scaling.

Edit/Save Matrix...

You can edit the compensation matrix and you can save the matrix to be used in another workspace.

(Acquisition Matrix)

If you compensated your data during acquisition on a new generation of instruments (DiVa, FC500 or the CyAn), the acquisition matrix will be available for editing.

(Compensation Matrices)

Apply the selected matrix to all currently-selected samples in the workspace. If a group is selected, then the matrix is applied to all samples in the group.

Go back to the overview of compensation.