3D segmentaion of grains, is it possible with this example image stack


I am at a real road block with this example stack

Several of the objects fold into each other, each thing should be a independent spherical wheat grain.

But they overlap and watersheding doesn’t seem to work. And for 3d shapes like this I have no idea what to do or how to proceed?

Any help, suggestions or ideas would be greatly appreciated

Hey @SirSharpest

So… I really don’t know how best to help you on this one ,but I think I can point you in a good direction… take a look at this great plugin: Morphological Segmentation. It might just be the tool you need to get the job done.

Hope this helps a bit at least!

eta :slight_smile:

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In this case and since the 3D image is binary, I recommend the Distance Transform Watershed 3D plugin, also included in MorphoLibJ.

I inverted the input image so the objects have 255 pixel value and the background is 0, then called the plugin with defaults parameters and obtained the following result:


This looks absolutely amazing!

Got a huge sample size to test this on, thank you so much.
Will let you know how successful this is.


Great! Just remember to invert the images because the plugin works assuming the segmented objects have intensity value 255 and background 0 :wink:

Yup, works beautifully for what I’ve been trying.
Does this support macro-ing? Tried recording it but didn’t seem to be picked up.

Weird, it does get recorded for me:

run("Distance Transform Watershed 3D", "distances=[Borgefors (3,4,5)] output=[16 bits] normalize dynamic=2 connectivity=6");