3D stack pore visualization


Hi guys ,
I have reconstructed a 3d volume from stack images. I am wondering if there is a way just to visualize the pores .

As you can see in the image, the darker area corresponds to pores and lighter areas are fiber layers. What if, i just want to see the pores as an object and nothing else . Is it possible ? There is one older post which does suggests it is possible !! Any help will be appreciated.
Kind Regards



Can you add a link here to the old forum post to which you are referring? It is still not so clear to me exactly what you want to visualize.

eta :slight_smile:


Dear @faruuk,

Maybe you can just try to invert your image, the pores will then be bright, so you can see them. Alternatively, but more complicated, you need to threshold the pores, then obtain a binary image and visualise it.

hope the helps




Hi etarena ,
Here is the link ,


Hi Thomas,
I did try to invert and see the pores but it does not really work , since it will still show the fibers as well. It just makes them appear other way around , i mean black for fibers and white for pores . I have replied one link to etarena , which does shows it is certainly possible but i am not sure that guy is even anymore active on this forum .


Hello @faruuk,

Maybe you can upload your 3D image somewhere so we can access it and better understand the problem?


Hi mate,
Its nice to see your reply. I have actually seen you very active in many of the posts . Great job !!
I am not well verse with imageJ yet , so ,I can upload stack of 100 images on dropbox and send the link , does it sounds ok ?


I have shared a link of image file. Its a binarized stack, which can be simply viewed in 3d viewer imageJ.


Best regards


Hello @faruuk!

Yes, a dropbox link would be great. You said you shared it but I don’t see it here, can you please edit your post again with the link?


Dropbox link to image data


It shows a broken icon , which is actually the link . I dont know why it looks like this :frowning:


Me neither, I edited it and fixed the problem by linking it to text :wink:


I had a look at your image and it looks like many of your pores got merged when you binarized the image. To better visualize it, I inverted the pixel values as suggested by @ThomasBoudier:

I guess you are interested in the original pores, so you would have to pre-process your image before to extract the individual pores using some of the tools suggested in the links you posted above.

If you share your original grayscale image, we can try to help you with that.


You are absolutely right, binarization is also a bit difficult in this sample.By the way i also tried to do the invert but it doesnt give me the desired results and as you have mentioned I am interested in original pores.
Here is the link.

I am already very thankful for your help.
Kind regards


It looks like your pores are also merged in the grayscale image. I tried the Morphological Segmentation plugin after converting the image to 8-bit. I recommend you to play with it and see if the results are satisfactory:


Thanks for the advice, i have this plugin so i will give it a go. I will let you know ,how it goes. Special thanks for your time. Really appriciate it.
Kind Regards