Converting a stacks of images into 3D, but the parts with lower value becomes as hole. How to fix it?


Hi, everyone,
I have got a serials of image stacks, generated from dividing of two other images stacks, However, after I using the 3D viewer plugin in the Fiji, the parts with lower value become as a hole.

I have tried the thresholding the images, yes, it turns out to be better some times, but still there are holes.

Could anyone give me some suggestions to fix this?

Here I post the stack images and converted 3D images.


many thanks!


I don’t understand. You are saying there shouldn’t be any holes? Wouldn’t that just produce a solid block?


Thank you very much @Andrew_Shum

Yes, there should be some holes, in some particular parts. I am sorry I have not clearly explained the problems. I mean, the parts within the “domains” should have a lower value, but not a hole.
I think that might be caused by the threshold problems.

I have fixed that by changing the threshold values.



I know you already found a solution and my apologies for such a delayed response. However, I thought it would be worth mentioning that you might consider using the “Close” operation depending on whether or not retaining the exact geometry is critical.


3q for this valuable suggestion.
It is also a solution.