Equivalent to Imaris surfaces in FIJI

Hi all,
I would like to create surfaces in FIJI the way Imaris makes them. So basically in Imaris one would set how smooth one wants the surface to be with a value for surface detail in µm and then there is basically a thresholding step and an some optional filters based on volume or shape for example.

So I found that using a 3D Gaussian filter and then converting to mask based on a threshold does the job in FIJI.

run("Smooth (3D)", "method=Gaussian sigma=15 use");
run("Convert to Mask", "method=Default background=Dark calculate black");

However on Imaris making non complex surfaces tends to be very quick but the 3D Gaussian tends to be quite time consuming in FIJI.
So my question is whether there are better ways of creating surfaces as Imaris does better than what I just described?

Thank you very much

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have you tried using clij to speed things up?


Fantastic !
Thank you very much. (And thank you @haesleinhuepf)
In my case the 3D blur went from 1,2 min to about a second.


Dont thank me, i’m just the messenger. Thank @haesleinhuepf who made it.

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Hey @Wilson_Adams,

thanks for advertising!

And hey @LPUoO,

CLIJ recently reached beta-phase. That means we are pretty confident that it’s bug free. Nevertheless, it’s software research. :wink: So if there is anything, let’s have a chat!


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