In this scenario, the user may or may not have generated a compensation matrix while collecting data on the flow cytometer. The user has collected FCS file data for single-stain (and unstained) fluorophore controls. Cytobank will automatically compute the compensation matrix using these controls, via the Autocompensation Wizard. To access the Autocompensation Wizard, enter the Working Illustration and click the "Edit" button next to the Compensation heading under Plot Controls on the left side of the page. Once you arrive on the Compensation page, click the "Automatic Compensation" link on the left, and follow the on-screen instructions to tell Cytobank which files correspond to your single-stain controls and unstained controls. When you have finished, the newly calculated compensation matrix will appear under the list of compensation files that you can select from the Illustration Page and from within the Gating applet.

View a short video tutorial demonstrating how to use the Autocompensation Wizard.