CellProfiler IdentifyObjects Manually - Outline inside or outside object?



First post here!

A quick question -

Planning to use IdentifyObjectsManually in CellProfiler to create nuclear and cell segmentation masks.

Can anyone confirm whether outlines are meant to be drawn outside or inside objects? i.e. should I be drawing my outline on pixels I deem to be contained at the outermost edge of my object but still part of my object or the pixels which sit directly outside my object?

Hope that makes sense!


The outlines are included in the object, so I would draw on the outermost edge. If you find it difficult on your setup for whatever reason to draw super-precise outlines and your major issue is merges and splits (rather than lacking a good marker for the objects in question), I’m also a fan of getting the edges “close-to-right”, then you can use ExpandOrShrinkObjects to shrink everything in a few pixels and IdentifySecondaryObjects to expand to the edge of the fluorescent border.

(We also have an EditObjectsManually module, if you don’t want to draw in every object by hand!)


Thanks Beth. That’s exactly what I needed.

Best wishes,



Hi Beth,

One more question about this module -

Is it possible to identify more than one class of object on an image on a single run of the CellProfiler IdentifyObjectsManually module?