3D coordinates of fluorescently labelled cells


I’m sorry if this is too basic for this forum but I’ve just started using ImageJ and I want to be able to do 3D spatial mapping of red fluorescently labelled cells in my organism i.e. identify each red fluorescent cell in my stack of images and return the 3D coordinates for each.

Is there a plugin which exists for this already please?

I’ve looked at 3D counter and Foci Picker3D but haven’t explored them in depth yet.

Thank you very much in advance, any help would be really great!

You need to segment your cells first. Try searching for 3d cell segmentation. One possible plugin is MorphoLibJ. There are also alternatives besides ImageJ, e.g. ilastik.

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