I am running FIJI v 1.51p on Max OS 10.10.5.
I'm having trouble adding overlays to multichannel hyperstacks, using a selection defined by an ROI from within the RoiManager. I initially encountered this problem when generating overlays from ROIs within a macro, but I have realized that the same problem also occurs from within the ImageJ GUI, which I have described below:
I have a two-channel hyperstack, and would like to add an overlay to both channels, using an ROI defined only by a feature in channel 2.
I define a selection based on some pixels in channel 2 and add this selection as an ROI to RoiManager.
I deactivate the option "Set stack positions" from within "Image > Overlay > Overlay Options...". According to the ImageJ documentation, this configuration should allow an overlay defined in one channel to be added to all channels in a multichannel hyperstack. (This option does work as documented when an overlay is made directly from a selection, without going through RoiManager.)
I select the ROI from within RoiManager.
I make the overlay using Image > Overlay > Add Selection... .
The result: the overlay only gets added to channel 2 and NOT to channel 1 under this configuration. (When the option "Set stack positions" is activated from within "Image > Overlay > Overlay Options...", then the overlay gets added to all channels of the hyperstack.)
This problem also occurs when an overlay is generated from an ROI defined in the other channel.