ROI inclusion analysis _ exclude Outer ROI with no inner ROI from export

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    deborakeller0@gmail.com May 29, 2019 at 3:21 pm

    Hi again,

     

    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

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