Interconnected pore segmentation

Hi all,

For my thesis I’m trying to find the volume and area of different porous structures, I’ve already created a binary image stack, see picture below.

I segmented this using the Morphological Segmentation tool (MorphoLibJ), which worked perfect for porosity’s up to around 20%. However, when the porosity is increased any further there are pores who touch both the top and bottom of the image stack. In other words they are interconnected all the way through. Which makes the (I assume watershed) algorithm think that it’s not part of the porous structure, see samples below.


40% porosity (black spots should be colored as well)


60% porosity (black spots should be colored as well)

Is there any way to segmentate all pores, so including all the black parts?

Any help or thought would be appreciated!

Thanks,
Sybren

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Figured it out myself, so for future references;

Add a white slide before and after your stack, run the segmentation, remove those two extra images again. Solved.

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