Background Subtraction Process Description

Background Subtraction Process Description:

Different fluorescence channels and imaging conditions can result in variable background fluorescence, which is fluorescence in areas where there is no fluorophore. To correct variations in this background level between channels (and between images), the average background intensity is subtracted from each image. The background area is determined using the background masks, which were created beforehand.

Parameter Descriptions:

Input Channels:

This allows you to select which channels you want to create background masks for. By default, all channels will have background masks created. These masks are generally used to perform background subtraction. Select the channels by clicking on them in the "Available Input Channels" box and then clicking "Select->" to move them to the "Selected Channels" box. You can unselect a channel by clicking the "Delete" button.

Background Mask Channels:

This allows you to select which channels to take background masks from for background subtraction. The default is to use the masks from the same channel that is being corrected. However, in the case that one channel has poor quality masks, you may use masks from a different channel to perform background subtraction on that channel. This is a valid alternative as long as both channels are spatially aligned within the background mask growth radius.