Segmentation of cells with nuclei and membrane signals

Hi @haesleinhuepf,

The parameters are described shortly in https://imagej.net/LimeSeg.html#Single_object_segmentation, there’s also the publication if you really want to… But I’d say you can try a bunch of values for d_0 (spacing between elements in pixel range : [1:1:10]) and f_pressure (“balloon force” range : [0:0.005:0.03]) and you’ll soon see if it is promising or not. You can send me a small cropped image with a few timepoint also. If it looks great, that could be part of some of the example scripts (multiple seeds + multiple timepoints) if you agree (https://github.com/NicoKiaru/LimeSeg/tree/master/src/main/resources/script-templates/LimeSeg) ?

Cheers,

Nico

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Awesome, that’s a great and detailed piece of documentation @NicoKiaru!:star_struck: I’ll give it a go!
Thanks!

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Hello, The parameter free segmentation is on its way to release, it needs only membrane channel and no pre-selected seeds for segmentation of multiple touching cells. It uses a subset of smartseeds algorithm tools. Stay tuned:

Here it is @imagejan

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