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Threshold Segmentation in TrakEM2

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arjundayal

Threshold Segmentation in TrakEM2

Hi,

I am using photoshop to highlight a certain region in my EM images and then registering these serial images using TrakEM2. I am now trying to create a 3D model of this region and am stuck on the manual segmentation step. The region that I want to segment is already segmented as it is a different color than the neighboring area. I would like to avoid having to redraw an outline around this area and was hoping for a way of telling TrakEM2 to use the obvious color difference as a way to segment the image. I have attached in example image to the post. I am interested in modeling the yellow region of the image without having to redraw all the outlines.

Arjun Dayal
M.D. Class of 2016
University of Chicago - Pritzker School of Medicine

arjundayal

Re: Threshold Segmentation in TrakEM2

Arjun Dayal
M.D. Class of 2016
University of Chicago - Pritzker School of Medicine

Albert Cardona-2

Re: Threshold Segmentation in TrakEM2

In reply to this post by arjundayal

Option 1: Create a script that processes each image so that the color is picked and kept and the rest is set to black. Set the script to every image from the right-click menu.

Option 2: filter your images so that the color of interest pops up. Rigth-click, then Adjust Images - Adjust image filters...

Then, use the pencil tool having an AreaList selected. See the manual.

What I would do: write a script to pick up the colored areas and add them to an arealist.

Albert

On Sep 3, 2013, at 12:35 AM, arjundayal <[hidden email]> wrote:

> Hi,
>
> I am using photoshop to highlight a certain region in my EM images and then
> registering these serial images using TrakEM2. I am now trying to create a
> 3D model of this region and am stuck on the manual segmentation step. The
> region that I want to segment is already segmented as it is a different
> color than the neighboring area. I would like to avoid having to redraw an
> outline around this area and was hoping for a way of telling TrakEM2 to use
> the obvious color difference as a way to segment the image. I have attached
> in example image to the post. I am interested in modeling the yellow region
> of the image without having to redraw all the outlines.
> <http://imagej.1557.x6.nabble.com/file/n5004623/sample.jpg>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Threshold-Segmentation-in-TrakEM2-tp5004623.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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Stephan Saalfeld

Re: Threshold Segmentation in TrakEM2

Hi Albert,

doesn't such import script for importing foreign annotations exist
somewhere? I remember vaguely that similar problems were solved for
Amira and Reconstruct:

https://groups.google.com/forum/#!topic/fiji-devel/iW35mArUV4M

http://fiji.sc/Reconstruct_Reader

And you once created something for Raju Tomer's data preserving label
names. No deeper insight into the matter though---sorry.

Best,
Stephan

On Wed, 2013-09-04 at 01:21 +0200, Albert Cardona wrote:

> Option 1: Create a script that processes each image so that the color is picked and kept and the rest is set to black. Set the script to every image from the right-click menu.
>
> Option 2: filter your images so that the color of interest pops up. Rigth-click, then Adjust Images - Adjust image filters...
>
> Then, use the pencil tool having an AreaList selected. See the manual.
>
> What I would do: write a script to pick up the colored areas and add them to an arealist.
>
> Albert
>
> On Sep 3, 2013, at 12:35 AM, arjundayal <[hidden email]> wrote:
>
> > Hi,
> >
> > I am using photoshop to highlight a certain region in my EM images and then
> > registering these serial images using TrakEM2. I am now trying to create a
> > 3D model of this region and am stuck on the manual segmentation step. The
> > region that I want to segment is already segmented as it is a different
> > color than the neighboring area. I would like to avoid having to redraw an
> > outline around this area and was hoping for a way of telling TrakEM2 to use
> > the obvious color difference as a way to segment the image. I have attached
> > in example image to the post. I am interested in modeling the yellow region
> > of the image without having to redraw all the outlines.
> > <http://imagej.1557.x6.nabble.com/file/n5004623/sample.jpg>
> >
> >
> >
> > --
> > View this message in context: http://imagej.1557.x6.nabble.com/Threshold-Segmentation-in-TrakEM2-tp5004623.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Albert Cardona-2

Re: Threshold Segmentation in TrakEM2

On Sep 4, 2013, at 8:49 AM, Stephan Saalfeld <[hidden email]> wrote:

> Hi Albert,
>
> doesn't such import script for importing foreign annotations exist
> somewhere? I remember vaguely that similar problems were solved for
> Amira and Reconstruct:
>
> https://groups.google.com/forum/#!topic/fiji-devel/iW35mArUV4M
>
> http://fiji.sc/Reconstruct_Reader
>
> And you once created something for Raju Tomer's data preserving label
> names. No deeper insight into the matter though---sorry.
>
> Best,
> Stephan

The importer works on labeled areas, that is, areas of homogeneous intensity value in single-channel images. As far as I understood, the images in question where originals with some areas painted on top. A custom approach is required.

Albert

>
>
> On Wed, 2013-09-04 at 01:21 +0200, Albert Cardona wrote:
>> Option 1: Create a script that processes each image so that the color is picked and kept and the rest is set to black. Set the script to every image from the right-click menu.
>>
>> Option 2: filter your images so that the color of interest pops up. Rigth-click, then Adjust Images - Adjust image filters...
>>
>> Then, use the pencil tool having an AreaList selected. See the manual.
>>
>> What I would do: write a script to pick up the colored areas and add them to an arealist.
>>
>> Albert
>>
>> On Sep 3, 2013, at 12:35 AM, arjundayal <[hidden email]> wrote:
>>
>>> Hi,
>>>
>>> I am using photoshop to highlight a certain region in my EM images and then
>>> registering these serial images using TrakEM2. I am now trying to create a
>>> 3D model of this region and am stuck on the manual segmentation step. The
>>> region that I want to segment is already segmented as it is a different
>>> color than the neighboring area. I would like to avoid having to redraw an
>>> outline around this area and was hoping for a way of telling TrakEM2 to use
>>> the obvious color difference as a way to segment the image. I have attached
>>> in example image to the post. I am interested in modeling the yellow region
>>> of the image without having to redraw all the outlines.
>>> <http://imagej.1557.x6.nabble.com/file/n5004623/sample.jpg>
>>>
>>>
>>>
>>> --
>>> View this message in context: http://imagej.1557.x6.nabble.com/Threshold-Segmentation-in-TrakEM2-tp5004623.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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arjundayal

Re: Threshold Segmentation in TrakEM2

In reply to this post by Albert Cardona-2

Hi Albert,

Thank you very much for your help! I wrote Java code that creates an Area object out of the yellow areas. How do I proceed to add it to the active AreaList in TrakEM2? Is there anything simpler than using Jython to call my Java code?

Thanks,
Arjun

Arjun Dayal
M.D. Class of 2016
University of Chicago - Pritzker School of Medicine

Albert Cardona-2

Re: Threshold Segmentation in TrakEM2

2013/12/25 arjundayal <[hidden email]>

> Hi Albert,
>
> Thank you very much for your help! I wrote Java code that creates an Area
> object out of the yellow areas. How do I proceed to add it to the active
> AreaList in TrakEM2? Is there anything simpler than using Jython to call my
> Java code?
>
> Thanks,
> Arjun
>

Arjun,

from java itself, or from jython: it doesn't matter.

From java you'd do, to add a specific Area to a Layer with id layer_id, to
all AreaList existing in the project:

import ini.trakem2.Project;
import ini.trakem2.display.*;

Project p = Project.getProjects().get(0);
LayerSet ls = p.getRootLayerSet();

Area a = ... ; // in world coordinates
long layer_id = ...;

for (AreaList ali : ls.getAll(AreaList.class)) {
Area local = new Area(a);
local.transform(ali.getAffineTransform());
ali.addArea(layer_id, local);
}

Hope the above helps.

Albert

>
>
>
> -----
> Arjun Dayal
> M.D. Class of 2016
> University of Chicago - Pritzker School of Medicine
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Threshold-Segmentation-in-TrakEM2-tp5004623p5005979.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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arjundayal

RE: Threshold Segmentation in TrakEM2

Thank you very much Albert! I think I'm all set now :)

Date: Thu, 26 Dec 2013 05:58:44 -0800
From: [hidden email]
To: [hidden email]
Subject: Re: Threshold Segmentation in TrakEM2

2013/12/25 arjundayal <[hidden email]>

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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Arjun Dayal
M.D. Class of 2016
University of Chicago - Pritzker School of Medicine