Background Mask Process Description

Background Mask Process Description:

This process uses the (previously created) masks, which label the foreground (i.e., fluorescent objects of interest), to create masks which label the background. To ensure that no foreground is included in these masks, the original masks are "grown" by a user-specified amount. This makes sure that the background mask is far away from any foreground objects.

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.

Growth Radius:

This parameter determines how much the masks will be "grown" before being used to create background masks. That is, any pixel which is further than this distance away from any mask objects will be considered background. If you have very little background area in your images, you can decrease this value to make sure that some background is included in the background masks.