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.