Colour-coding ROI with a LUT corresponding to the number of spots inside

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  • DavidG November 8, 2019 at 11:58 am

    Hi everyone,

     

    I have a protocol to count spots inside nuclei, and I would like to colour-code the nuclei ROI, with a LUT that is linked to the number of spots inside each nuclei. The bloc “Color ROI” does this, but for other calculated parametres (area, position, circularity etc).

    At the moment I can not find a way to input the number of spots per nuclei into “Color ROI”.

    Is there a way to do this please? Ideally it would come from the “ROI Inclusion Analysis” results, column F is ‘nb. enclosed ROI’.

    Many thanks in advance!

     

    David

    Stephane Dallongeville November 26, 2019 at 3:54 pm

    Hi DavidG,

    In fact to do that easily using the Color ROI plugin we need to implement a new ROI Descriptor counting the number of enclosed ROI. Currently there is not that kind of ROI Descriptor as Descriptors are supposed to compute a value relative to a specific ROI. Still that’s possible to do as the compute method from ROI descriptor interface receive have the Sequence information to compute its result (to compute intensity value for instance) so we could retrieve all ROI from the Sequence that way. Honestly that is not a very elegant way of doing that, a better way would be to have a new kind of ROI Descriptor computed against a list of ROI. Still at this point, it’s not probably too hurtful to try that (i’m just afraid about the computing time when you have many ROIs in your sequence).
    We will probably give a shot about it soon as indeed it would be really useful to have that descriptor (intersected ROI / contained ROI) 🙂

    Best,

    – Stephane
    DavidG December 5, 2019 at 11:54 am

    Thanks in advance Stephane, that would be a useful feature to have!

    Let me know if you can make it work!

    Merci 🙂

    David

    Stephane Dallongeville December 6, 2019 at 4:43 pm

    Indeed, i think it’s a nice feature too, it’s why you will have it in next version of Icy 🙂 Descriptors will be called “Intersected” and “Contained” representing respectively the number of Intersected ROI(s) and the number of contained ROI(s).

    Best,

    – Stephane

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