3D Pore Network Segmentation, Particle Size Analysis

Hi, I am looking to segment a 3D image, constructed from a stack of 2D images, into individual particles to analyze pore and particle size. Ideally the segmentation would work similarly to the 2D adjustable watershed segmentation.

I have used the TrakEM2 plugin to segment the pores and particles as an area list as shown in the figure below:

From this point I can create a 3D volume mesh with the 3D viewer, however searching through the ImageJ wiki and the forums I have not been able to find anyway to segment the aglomerates of a 3D volume.

My next thought was to create an image stack from the area list, convert it to a binary image and use the 3D watershed split plugin to segment the pores. However, this does not seem to segment any of the pores.

Can anyone suggest a method for segmenting 3D volumes or a stack of 2D images?


Hello @graemec,

You might want to give a try to the Morphological Segmentation plugin which is part of the MorphoLibJ library.


Hello @iarganda,
Thank you for the quick reply. The Morphological Segmentation plugin did not complete the segmentations as I wanted, however I found another forum post using 3D watershed segmentation that worked well. Which plugins are for cell segmentation and volume measurement in 3D


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