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?