MaskObjects

Mask Objects removes objects outside of a specified region or regions.

This module allows you to delete the objects or portions of objects that are outside of a region (mask) you specify. For example, after identifying nuclei and tissue regions in previous Identify modules, you might want to exclude all nuclei that are outside of a tissue region.

If using a masking image, the mask is composed of the foreground (white portions); if using a masking object, the mask is composed of the area within the object. You can choose to remove only the portion of each object that is outside of the region, remove the whole object if it is partially or fully outside of the region, or retain the whole object unless it is fully outside of the region.

Available measurements

Parent object measurements:

Count: The number of new masked objects created from each parent object.

Masked object measurements:

Parent: The label number of the parent object.
Location_X, Location_Y: The pixel (X,Y) coordinates of the center of mass of the masked objects.

Settings:

Select objects to be masked

Select the objects that will be masked (that is, excluded in whole or in part based on the other settings in the module). You can choose from any objects created by a previous object processing module, such as IdentifyPrimaryObjects, IdentifySecondaryObjects or IdentifyTertiaryObjects.

Name the masked objects

Enter a name for the objects that remain after the masking operation. You can refer to the masked objects in subsequent modules by this name.

Mask using a region defined by other objects or by binary image?

You can mask your objects by defining a region using objects you previously identified in your pipeline (Objects) or by defining a region based on the white regions in a binary image (Image).

Select the masking object

Select the objects that will be used to define the masking region. You can choose from any objects created by a previous object processing module, such as IdentifyPrimaryObjects, IdentifySecondaryObjects, or IdentifyTertiaryObjects.

Select the masking image

Select an image that was either loaded or created by a previous module. The image should be a binary image where the white portion of the image is the region(s) you will use for masking. Binary images can be loaded from disk using the NamesAndTypes module by selecting "Binary mask" for the image type. You can also create a binary image from a grayscale image using ApplyThreshold.

Invert the mask?

This option reverses the foreground/background relationship of the mask.

Select No for the mask to be composed of the foregound (white portion) of the masking image or the area within the masking objects.
Select Yes for the mask to instead be composed of the background (black portions) of the masking image or the area outside the masking objects.

Handling of objects that are partially masked

An object might partially overlap the mask region, with pixels both inside and outside the region. MaskObjects can handle this in one of three ways:

Keep overlapping region: Choosing this option will reduce the size of partially overlapping objects. The part of the object that overlaps the region will be retained. The part of the object that is outside of the region will be removed.
Keep: If you choose this option, MaskObjects will keep the whole object if any part of it overlaps the masking region.
Remove: Objects that are partially outside of the masking region will be completely removed if you choose this option.
Remove depending on overlap: Determine whether to remove or keep an object depending on how much of the object overlaps the masking region. MaskObjects will keep an object if at least a certain fraction (which you enter below) of the object falls within the masking region. MaskObjects completely removes the object if too little of it overlaps the masking region.

Fraction of object that must overlap

(Used only if removing based on a overlap)
Specify the minimum fraction of an object that must overlap the masking region for that object to be retained. For instance, if the fraction is 0.75, then 3/4 of an object must be within the masking region for that object to be retained.

Numbering of resulting objects

Choose how to number the objects that remain after masking, which controls how remaining objects are associated with their predecessors:

Renumber: The objects that remain will be renumbered using consecutive numbers. This is a good choice if you do not plan to use measurements from the original objects; your object measurements for the masked objects will not have gaps (where removed objects are missing).
Retain:: The original labels for the objects will be retained. This allows any measurements you make from the masked objects to be directly aligned with measurements you might have made of the original, unmasked objects (or objects directly associated with them).

Retain outlines of the resulting objects?

Select Yes to retain the outlines of the new objects for later use in the pipeline. For example, a common use is for quality control purposes by overlaying them on your image of choice using the OverlayOutlines module and then saving the overlay image with the SaveImages module.

Name the outline image

(Used only if the outline image is to be retained for later use in the pipeline)
Enter a name for the outlines of the identified objects. The outlined image can be selected in downstream modules by selecting them from any drop-down image list.

Module: MaskObjects