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

3d
segmentation
Tags: #<Tag:0x00007fd53f498560> #<Tag:0x00007fd53f4983a8>

#1

Hello,

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


#2

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:


#3

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:


#4

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.
Thanks!


#5

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


#6

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.


#7

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");