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In need of help with a Fiji segmentation project!

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Bbnation1234

In need of help with a Fiji segmentation project!

Hi everyone! I am new to Fiji and this is my first time using a photo-editing program aside from some basic Photoshop. I just recently joined a research group, and I wont go into exact details of what it entails but I am working on a project with MLO mammogram images on Fiji. The photos show a black background, the actual breast material, and a section of the pectoral muscle. I need to find a method to accurately "crop" or section the breast from the background and the pectoral muscle without manually having to go in and use the drawing tool to section it off. (Like making a mask for it and cropping the other sections out so we are only left with the important breast part.) I also need this method to work when applied to a large file of different mammogram images.

So far I have been playing around with the Trainable Weka Segmentation plugin, and I haven't quite gotten the image segmented like I need to. If anyone could offer any kind of advice or help me in any way, it would be greatly appreciated! I am sorry for any incorrect terminology, but like I said previously, I am new to all this!

Please dont hesitate to ask for any clarification if its needed! Thanks so much for taking the time to read my post!

cromatina

Re: In need of help with a Fiji segmentation project!

Hi Amber,

I'm also quite new using ImageJ but I think I can help you a bit. I have
used the Segmentation Editor to segment my structures. If you open your
images in the segmentation editor first you can use the drawing tools to
encircle your desired structure. Now you can press T (threshold) and set
the values which highlight only the pixels that correspond to your
structure. At this point you can paint the zone, or, go to another slice
and do the same. When you have selected the pixels of interest in both
slices you can press I (Interpolate) and then it will interpolate the
selected zone in the region between the 2 slices.
Segmentation editor: http://fiji.sc/Segmentation_Editor
Have a look to this video: https://www.youtube.com/watch?v=tC-b-BFq6jk

Hope this helps!

2015-07-14 16:19 GMT+02:00 Bbnation1234 <[hidden email]>:

> Hi everyone! I am new to Fiji and this is my first time using a
> photo-editing
> program aside from some basic Photoshop. I just recently joined a research
> group, and I wont go into exact details of what it entails but I am working
> on a project with MLO mammogram images on Fiji. The photos show a black
> background, the actual breast material, and a section of the pectoral
> muscle. I need to find a method to accurately "crop" or section the breast
> from the background and the pectoral muscle without manually having to go
> in
> and use the drawing tool to section it off. (Like making a mask for it and
> cropping the other sections out so we are only left with the important
> breast part.) I also need this method to work when applied to a large file
> of different mammogram images.
>
> So far I have been playing around with the Trainable Weka Segmentation
> plugin, and I haven't quite gotten the image segmented like I need to. If
> anyone could offer any kind of advice or help me in any way, it would be
> greatly appreciated! I am sorry for any incorrect terminology, but like I
> said previously, I am new to all this!
>
> Please dont hesitate to ask for any clarification if its needed! Thanks so
> much for taking the time to read my post!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/In-need-of-help-with-a-Fiji-segmentation-project-tp5013556.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ctrueden

Re: In need of help with a Fiji segmentation project!

In reply to this post by Bbnation1234

Hi Amber,

> I need to find a method to accurately "crop" or section the breast
> from the background and the pectoral muscle without manually having to
> go in and use the drawing tool to section it off.

Could you please post a sample image (e.g., share a link via Dropbox),
along with a cropped or otherwise annotated version showing your desired
result?

Regards,
Curtis

On Tue, Jul 14, 2015 at 9:19 AM, Bbnation1234 <[hidden email]>
wrote:

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Bbnation1234

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.jpg

http://i288.photobucket.com/albums/ll183/Bbnation1234/Mobile%20Uploads/image_zpsq7fqmbbw.jpg

The 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

Krs5

Re: In need of help with a Fiji segmentation project!

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.jpg

http://i288.photobucket.com/albums/ll183/Bbnation1234/Mobile%20Uploads/image_zpsq7fqmbbw.jpg

The 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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View this message in context: http://imagej.1557.x6.nabble.com/In-need-of-help-with-a-Fiji-segmentation-project-tp5013556p5013571.html
Sent from the ImageJ mailing list archive at Nabble.com.

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