Spot detector: how to detect spots of different sizes?

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  • Audrey Cochard


    I am trying to use the spot detector tool to detect fluorescent spots in cells. Depending on the cells, I can have a few quite big spots (around 3µm²) or numerous small spots (up to 0,1µm²), and in a same cell the spots can be of different sizes. I can’t find the good settings to detect all my spots: spots close to one another are often detected together, but if I change the settings, some spots are nor longer detected. Here is an example of a cell I can have: as you can see numerous spots are detected together. I can remove these ROI and circle the spots by myself, but I wonder if there is a faster solution. Moreover, as I want to extract the number and sizes of the spots, I would like to find a setting that could fit the different cells to obtain consistent sizes. Would anyone know a way to determine good settings ?

    Thank you very much,


    Stephane Dallongeville

    Hi Audrey,

    Unfortunately that is a limitation of the Spot Detector plugin, it’s not really designed to detect spots with important difference in size.

    But you can use the protocol to adapt this and make several spot detection and combine the results. You can see an example with the protocol “Spot Detector scale 2 and scale 3” which is available online. Just type its name in the top search bar of Icy, you should be able to access it 🙂

    Hope that helps !

    – Stephane


    Victor Breton

    Hello Audrey,

    I had the same problem few times ago. What I did to solve this problem was to use different parameters of spot detector on the same image. Found 2 or 3 Spot Detector parameters which could englobe your whole spots (which are also separeted as in your picture) and use the Boolean operation in “Protocol”. The result will be to have different size of spots and for them which are superposed (because they will be detected with both of 2 parameters) they will be merge in one. Hope I help you atleast a bit, good luck for the rest =)


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