I am doing tracking of nuclei and spots and ROI inclusion analysis.
I have several cells that are not expressing the spot marker and I would like to ideally:
remove the Nuclei_ROI that have no Spot_ROI inside (or no GFP intensity) to avoid exporting data I don’t need
go back to nuclei ROI and remove the discarded ROI from the sequence screenshot.
basically I would like use ROI in channel 2 – measure channel 1 intensity within that ROI and discard ROI with intensities in Channel1< threshold, but unsure how and where to fit it (after inclusion analysis?)
The protocol I use is the following (simplified)
1- active contour on nuclei Channel 2-> generate OuterROI (except touching boundaries and <1500px)
-> export nuclei Stats
2- use the Nucleus_ROI to restrict spot detector in channel 1
3- ROI inclusion analysis
4- export Spot stats, Inclusion analysis and sequence screenshots