Individual object mask export


One thing that would really help, and I don’t know if this is already possible, would be export the individual masks of recognised objects. These could then be used in external image processing that CellProfiler is not capable of.



Hi Nicholas,

In SaveImages, you can export the label matrix for a given object set by selecting “Objects” for “Select the type of image to save”. This will produce an image in which the pixels comprising an object are given a unique index. Is this what you looking for?