Cytobank automatically detects any compensation matrix within your files and uses it for compensation. This compensation is referred to as the "File-Internal Compensation".

If your files do not have a compensation matrix within them (e.g. they were hardware compensated), Cytobank will detect this and not apply compensation even when the compensation is set to "File Internal Compensation".

If you want to define a new software compensation matrix to apply to all the files in an illustration, click on "Edit" next to the compensation control in the Illustration. This will take you to a page where you can create and edit compensation matrices.

To create a new compensation matrix by importing the matrix within a file and then editing it, choose the seed file next to the text that says "Import compensation matrix." Cytobank will then pull any compensation matrix from this file and allow you to edit it.

To create a new compensation matrix from scratch, select a seed file next to the text for "New Compensation". Cytobank will then ask you to select the channels that you want to be able to compensate. Check the channels you wish to be included in the compensation matrix. Cytobank will then create a blank compensation matrix where all the values are 0 (no compensation). You can then edit the values as needed.