Posted by
Krs5 on
Jul 16, 2015; 9:42am
URL: http://imagej.273.s1.nabble.com/In-need-of-help-with-a-Fiji-segmentation-project-tp5013556p5013591.html
Dear Amber,
The code below selects only the breast tissue in the image you send. You probably have to make some changes to the settings when working with the original images but it gives you an idea what is possible.
run("Duplicate...", "title=double");
run("8-bit");
setAutoThreshold("Mean dark");
setThreshold(23, 53);
run("Convert to Mask");
run("Options...", "iterations=5 count=1 black do=Nothing");
run("Dilate");
run("Fill Holes");
run("Erode");
run("Analyze Particles...", "size=25000-Infinity add");
close();
roiManager("select", 0);
setBackgroundColor(0, 0, 0);
run("Clear Outside");
run("Select None");
Best wishes
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Bbnation1234
Sent: 15 July 2015 15:32
To:
[hidden email]
Subject: Re: In need of help with a Fiji segmentation project!
Hi Curtis!
I currently don't have access to a computer so at the moment I can't send you a quality example like I could otherwise.. But on my phone I tried to show the different regions on a mammogram image.
http://i288.photobucket.com/albums/ll183/Bbnation1234/Mobile%20Uploads/image_zpsvyrhe06v.jpghttp://i288.photobucket.com/albums/ll183/Bbnation1234/Mobile%20Uploads/image_zpsq7fqmbbw.jpgThe first is the original image. In the second image, the background is marked with green, and the pectoral muscle is marked with blue. I basically want both of the colored sections gone so that I am left with just the breast. I was unsuccessful using the segmentation plugin that I previously mentioned because part of the breast tissue is the same shade (? Again I am sorry for any incorrect terminology haha) as the pectoral muscle. So within the breast, there would be a segment that would be marked in the same class as the pectoral muscle, which is obviously a problem because we need to be left with the entire breast material.
I will have access to a better example photo later on, so if what I am posting isn't good enough please let me know and I will send a better one!
Amber
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