Posted by
Jeremy Adler on
URL: http://imagej.273.s1.nabble.com/multi-phase-segmentation-marker-controlled-watershed-tp5023107p5023109.html
You want to identify 4 different materials -
how do they differ, size/volume, shape, texture, fluorescence, elemental composition?
Their differences are the basis for separating them.
I would also suggest considering Multi Otsu thresholding, unlike many segmentation methods which divides the image into two areas based on the histogram of the image, Multi Otsu allows for up to 5 divisions.
Jeremy Adler
BioVis
Uppsala U
-----Original Message-----
From: ImageJ Interest Group <
[hidden email]> On Behalf Of PatrIM
Sent: Monday, March 30, 2020 11:00 AM
To:
[hidden email]
Subject: multi phase segmentation marker-controlled watershed
Hi
I am working with a 3D image of a soil which contains 4 different materials.
I would like to segment it in 4 phases. I read that watershed works well so I am trying to use marker-controlled watershed, the one according with its description requires
-The Input image: a 2D or 3D grayscale image to flood, usually the gradient of an image.
-The Marker image: an image of the same dimensions as the input containing the seed points or markers as connected regions of voxels, each of them with a different label. They correspond usually to the local minima of the input image, but they can be set arbitrarily.
For the input I generated a gradient using morpholobj/morphological filters
(3D)
But for the Marker I am having problems. I don’t know how to generate an appropriate 3D image. Making use of global segmentation I generated an image of 4 phases, expecting it could work as my marker. However giving this image and my gradient to marker-controlled watershed it gives me back as a result the marker 3D image.
Do you how can I generate and appropriate marker? Or how can I obtain my segmentation in 4 phases?
Thanks in advance
--
Sent from:
http://imagej.1557.x6.nabble.com/--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlNär du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här:
http://www.uu.se/om-uu/dataskydd-personuppgifter/E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html