CP3 IdentifyTertiaryObjects retain outlines missing



Hi. I’ve just updated toCP3 from 2.2 on a mac. One of my previous projects had tertiary objects identified and in v2.2 these were retained and I later saved the image. Opening the project in v3 however, and the option to retain outlines and name them is no longer present. I tried re-inserting the module from scratch and it still doesn’t show up. According to the help: http://cellprofiler.org/manuals/current/IdentifyTertiaryObjects.html this should be there still.

Can anyone tel me if this is just a bug to be ironed out, possibly a mac specific error, or if it is a deliberate removal of functionality? In the interim, my project works fine as long as I remove the SaveImages module that was pointing to the now non existent outline image.




Hi Glyn,

As discussed here, that functionality was intentionally removed; you can make the outline image though by using OverlayOutlines. Sorry for the confusion!


Thanks bcimini, and apologies: I searched the forum, but didn’t look at the blog. I’ll alter my project to obtain the outlines. Perhaps a ‘What’s New’ link in the CP splash screen in the ‘Need more help’ section, in case other users don’t spot this conversation?

Thanks again. Glyn