Importing Predefined Primary and Tertiary Objects into CellProfiler



If I have the nucleus and cell boundaries as an output layer from machine learning algorithm, then can I use those locations (Nucleus and Cytoplasm areas) in CellProfiler to get the median intensity of my original images in those predefined areas?

The reason for using my own predefined Nucleus and Cytoplasm is that CellProfiler couldn’t identify the primary, secondary and tertiary objects properly and breaks each cell apart into couple of cells. However, we could identify the Nucleus and Cytoplasm areas of our images and we want import them into CellProfiler and read the Intensity of our images in those Objects.

Thanks so much,


Yes, you can import segmentations into CellProfiler by specifying the type of image as Objects within the NamesAndTypes module. Just make sure your label image is a uint16 and independent objects have a unique integer value. Once imported into a pipeline, two sets of objects from two label images can be related using the RelateObjects module.