Fill holes  
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Menu:   Processing > Morphology… > Connectivity->Fill holes  
Script:   fill  
Use this command to fill out background holes in objects in multiphase images
. The function uses a 4-connected "city-block" neighborhood for background identification.

If you choose this command, the following options will become available:

Displays the input image frame number. If you want to process another image, type or select the corresponding value.  

Displays the number of the frame in which the output image will be created. Depending on the Preferences. ImageWarp will set it either to the first available value or to the Input frame number. Type or select another value if you want the output image to be created in a different frame.  
Select this check box to watch the Preview of the output image.  

Lets you choose one of the following modes:  
Click Fast to use the algorithm optimized for binary images. Selecting this mode for multiphase images with objects of different phases enclosed into each other may result in loosing the original phase information.  
Click Topologic to use the algorithm optimized for multiphase images with parent-child relations between objects of different phases.