Generating surfaces via interpolation between image slices for a binary stack using ImageJ

Hi all,

I am a university undergraduate and have hit a road block in finding a means of interpolating between my image slices in imageJ. I can export my stack as an STL but the regions between slices have a simple extrusion along the z axis linearly to the next slice.

I’ve used Meshlab and SpaceClaim in attempts to smooth the surfaces, however this feels very arbitrary when focusing on the regions that are visually more static from one slide to the next and the skin wrapping tool erodes fine detail I would like to preserve.

Is there a Plugin Macro or means of using existing ImageJ commands to enable an stl export with a smooth surface?

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Hey @Tyson97,

I think resampling, blurring and thresholding your binary dataset could do the trick…

Would you mind sharing an example dataset so that we could play a bit with it?

Cheers,
Robert

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Thank you for the response and sincere apologies on the late reply, I would love to but the information is part of an academic project and so I’m unable to share the image stack with a broader academic audience. I will take your thoughts into consideration moving forward.

Thank you again for the advice Robert

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