X-y alignment - can I bypass using the module?

In a previous post I brought up an x-y alignment issue. Mark added the issue to the tracker: github.com/CellProfiler/CellProfiler/issues/758

I was wondering if I can somehow bypass the issue in the meantime, but increasing the size of the nucleus after primary segmentation.
At the moment I identify the secondary object with Distance - N. Can I somehow make it identify the secondary object by starting X pixel outside the primary object, thus enlarging the nuclear mask? Or just make the secondary object start farther from the border of the nucleus? (same effect)

Thanks,
Avi


scanr_v1_noAlign.cp (13.7 KB)

[quote=“rogueiam”]I was wondering if I can somehow bypass the issue in the meantime, but increasing the size of the nucleus after primary segmentation.
At the moment I identify the secondary object with Distance - N. Can I somehow make it identify the secondary object by starting X pixel outside the primary object, thus enlarging the nuclear mask? Or just make the secondary object start farther from the border of the nucleus? (same effect)[/quote]

This is doable, though you would have to be the judge of whether this actually compensates well for the alignment problem.

You can use the ExpandOrShrinkObjects module to expand the primary object by N pixels, and then use IdentifySecondary to use the expanded nuclei as the seeding object.
-Mark