Exclude Objects


I have a mixed population with GFP labelled and unlabelled cells. Now I want to exclude the GFP positive cells and go on with the analysis only with the unlabelled cells only. I Identified first the nuclei then using secondary identification the GFP labelled cells. Now I want to cut the GFP positive cells away.
With CP1 I used Module Exclude and now in CP2 it is called MaskObject.
My Problem is: I want to keep the nuclei OUTSIDE of the masked region, not inside of this. In other words I want to use the nuclei that are not in the GFP positive cells. Is there a tool to invert the region or could you build a additional feature to choose exactly to ones outside the mask?

Thank you


1 Like


This is a good point- we should add an “Invert the mask” option to MaskObjects. For now, instead of MaskObjects, use MaskImage, select Use Objects (and then pick the GFP labelled-cells) and check ‘Invert the Mask’. This will give you an image with the GFP labelled-cells cut away.



Thanks for the answer. For the moment I use CP2 (CP3 just adds minutes and never ends). When I use MaskImage I get a binary image. How can I have the gfp negative nuclei with their intensities?



Just to clarify, we only have two versions of CellProfiler: 1.0.XXXX (all the matlab versions) and 2.0. There’s no 3.0 yet. As for using MaskImage as I directed you to, it should produce a grayscale image with your gfp-positive cells masked out (set to zero). Do you mind attaching your pipeline so we can see what’s up?


For those interested: An “Invert the mask” option is available in MaskObjects with the latest version of CellProfiler 2.0.