Galaxy |

RelateObjects (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

Parent objects:

Parent objects are defined as those objects which encompass the child object. For example, when relating speckles to the nuclei that contain them, the nuclei are the parents.

Child objects:

Child objects are defined as those objects contained within the parent object. For example, when relating speckles to the nuclei that contains them, the speckles are the children.

Calculate per-parent means for all child measurements?:

Select 'Yes' to calculate the per-parent mean values of every upstream measurement made with the children objects and store them as a measurement for the parent. This module must be placed after all the measure modules that make measurements of the children objects.

Calculate child-parent distances?:

Choose the method to calculate distances of each child to its parent. For example, these measurements can tell you whether nuclear speckles are located more closely to the center of the nucleus or to the nuclear periphery.
- None: Do not calculate any distances. This saves computation time.
- Minimum: The distance from the centroid of the child object to the closest perimeter point on the parent object.
- Centroid: The distance from the centroid of the child object to the centroid of the parent.
- Both: Calculate both the Minimum and Centroid distances.

Do you want to save the children with parents as a new object set?:

Select 'Yes' to save the children objects that do have parents as new object set. Objects with no parents will be discarded.

Enter a name for the output object:

What it does

RelateObjects assigns relationships; all objects (e.g., speckles) within a parent object (e.g., nucleus) become its children. This module allows you to associate child objects with parent objects. This is useful for counting the number of children associated with each parent, and for calculating mean measurement values for all children that are associated with each parent. An object will be considered a child even if the edge is the only partly touching a parent object. If a child object is touching multiple parent objects, the object will be assigned to the parent with maximal overlap. For an alternate approach to assigning parent/child relationships, consider using the MaskObjects module. If you want to include child objects that lie outside but still near parent objects, you might want to expand the parent objects using ExpandOrShrink or IdentifySecondaryObjects.

Input

Existing CellProfiler pipeline file (.cppipe) or generated by linking CellProfiler tools.

Output

The input CellProfiler pipeline file (.cppipe) in addition to the settings of this module.

IMPORTANT

The first tool in a CellProfiler workflow has to be Starting modules and the last one CellProfiler. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.