Re: IMAGEJ Digest - 2 Apr 2012 to 3 Apr 2012 (#2012-89)

[Mitzner, Wayne]

Mike, I can't help you, but if you do figure this out, please let me know,
since I'd be very interested in doing the same.
-wayne

>Date:    Tue, 3 Apr 2012 10:46:36 -0400
>From:    Michael Sullivan <[hidden email]>
>Subject: 3D ROI generation
>
>Hi. I'm in need of some direction.  It has been a while since I've made
>any extensive use of imageJ.  I have a set of dicom files (e.g.
>export-0001.dcm) from a microCT of mice lungs.  I need to build a 3D ROI.
>
>The process as I imagine it is to progress through the set of images
>drawing 2D ROIs as I go -- hopefully I don't need to draw ROIs on every
>slice.  I then want to construct the 3D ROI and view it in a tool that
>will allow me to 1) change the angle of the three axis, 2) Allow me to
>select the color of the 3D ROI,   3) Allow me to have more than one 3D
>ROI visible in different colors, and 4) Save the image to a TIF or JPEG.
>
>I've been looking at the plugins available but feel like I'm drinking
>from a fire-hose.  I'm hoping that someone might direct me to the best
>place to start.
>--- Mike

[Albert Cardona-2]

El 4 d’abril de 2012 7:55, Mitzner, Wayne <[hidden email]> ha escrit:

> Mike, I can't help you, but if you do figure this out, please let me know,
> since I'd be very interested in doing the same.
> -wayne
>
>>Date:    Tue, 3 Apr 2012 10:46:36 -0400
>>From:    Michael Sullivan <[hidden email]>
>>Subject: 3D ROI generation
>>
>>Hi. I'm in need of some direction.  It has been a while since I've made
>>any extensive use of imageJ.  I have a set of dicom files (e.g.
>>export-0001.dcm) from a microCT of mice lungs.  I need to build a 3D ROI.
>>
>>The process as I imagine it is to progress through the set of images
>>drawing 2D ROIs as I go -- hopefully I don't need to draw ROIs on every
>>slice.  I then want to construct the 3D ROI and view it in a tool that
>>will allow me to 1) change the angle of the three axis, 2) Allow me to
>>select the color of the 3D ROI,   3) Allow me to have more than one 3D
>>ROI visible in different colors, and 4) Save the image to a TIF or JPEG.
>>
>>I've been looking at the plugins available but feel like I'm drinking
>>from a fire-hose.  I'm hoping that someone might direct me to the best
>>place to start.
>>--- Mike

Hi Michael and Wayne,

I would do this in TrakEM2:

http://www.ini.uzh.ch/~acardona/trakem2.html

The set of ROIs is called "area list". You may draw an area at, say,
every 5th slice, and then interpolate in between.

http://www.ini.uzh.ch/~acardona/trakem2_manual.html#arealists

The manual has fallen behind a bit. The interpolation option is in the
right-click menu, when you have an "area list" selected. At the top,
"Areas - Intepolate [...]" offers various options.

When you have drawn the areas, then right-click and select "Show in
3D", which opens the 3D Viewer with a mesh showing the volume.

Take good care of calibrating the volume:

http://www.ini.uzh.ch/~acardona/trakem2_manual.html#calibration

There are video tutorials to get you started:

http://fiji.sc/wiki/index.php/TrakEM2_tutorials

Hope that helps.

Albert

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

[Michael Doube-3]

Hi Mike,

>> export-0001.dcm) from a microCT of mice lungs.  I need to build a 3D ROI.

At the moment the only realistic way to make a 3D ROI is to use a series
of 2D ROIs. Alternatively you can make a binary mask and manipulate
that, e.g. in the 3D Viewer.

>> The process as I imagine it is to progress through the set of images
>> drawing 2D ROIs as I go -- hopefully I don't need to draw ROIs on every
>> slice.

Check out the ROI interpolator in BoneJ, which does exactly that.
http://bonej.org/utilities

The rest is a bit beyond what I've needed, but perhaps someone else can
help.

Michael

[Krs5]

Mike and Wayne

You could try to use the Segmentation Editor. This allows you to draw 2D ROIs on some slices and will fill in the ROIs in the slices in between. You can then view the results in the 3D viewer.

Kees
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Mitzner, Wayne [[hidden email]]
Sent: 04 April 2012 12:55
To: [hidden email]
Subject: Re: IMAGEJ Digest - 2 Apr 2012 to 3 Apr 2012 (#2012-89)

Mike, I can't help you, but if you do figure this out, please let me know,
since I'd be very interested in doing the same.
-wayne

>Date:    Tue, 3 Apr 2012 10:46:36 -0400
>From:    Michael Sullivan <[hidden email]>
>Subject: 3D ROI generation
>
>Hi. I'm in need of some direction.  It has been a while since I've made
>any extensive use of imageJ.  I have a set of dicom files (e.g.
>export-0001.dcm) from a microCT of mice lungs.  I need to build a 3D ROI.
>
>The process as I imagine it is to progress through the set of images
>drawing 2D ROIs as I go -- hopefully I don't need to draw ROIs on every
>slice.  I then want to construct the 3D ROI and view it in a tool that
>will allow me to 1) change the angle of the three axis, 2) Allow me to
>select the color of the 3D ROI,   3) Allow me to have more than one 3D
>ROI visible in different colors, and 4) Save the image to a TIF or JPEG.
>
>I've been looking at the plugins available but feel like I'm drinking
>from a fire-hose.  I'm hoping that someone might direct me to the best
>place to start.
>--- Mike

[Paul Johnston]

Look into osirix for this task. You can load your ct stack, define 2d rois
along axial sections, and the algorithm will interpolate the missing info
to create a 3d volume. People use it to make volumetric measurements of
liver tumors, aneurysms, etc. there is a youtube video that shows how to do
it, but I don't have the link hand.

Pcj
On Apr 4, 2012 8:06 AM, "Mitzner, Wayne" <[hidden email]> wrote:

> Mike, I can't help you, but if you do figure this out, please let me know,
> since I'd be very interested in doing the same.
> -wayne
>
> >Date:    Tue, 3 Apr 2012 10:46:36 -0400
> >From:    Michael Sullivan <[hidden email]>
> >Subject: 3D ROI generation
> >
> >Hi. I'm in need of some direction.  It has been a while since I've made
> >any extensive use of imageJ.  I have a set of dicom files (e.g.
> >export-0001.dcm) from a microCT of mice lungs.  I need to build a 3D ROI.
> >
> >The process as I imagine it is to progress through the set of images
> >drawing 2D ROIs as I go -- hopefully I don't need to draw ROIs on every
> >slice.  I then want to construct the 3D ROI and view it in a tool that
> >will allow me to 1) change the angle of the three axis, 2) Allow me to
> >select the color of the 3D ROI,   3) Allow me to have more than one 3D
> >ROI visible in different colors, and 4) Save the image to a TIF or JPEG.
> >
> >I've been looking at the plugins available but feel like I'm drinking
> >from a fire-hose.  I'm hoping that someone might direct me to the best
> >place to start.
> >--- Mike
>