ROI across slices

[mooseo]

I'm trying to do a simple analysis of density across a stack of ct images. Unfortunately, my ROI is simple to define in one plane, but challenging in the plane in which the volume is sliced. Essentially, I want a cylinder that goes through my object. If I rotate my object in the volume viewer, I can draw a circle around my region of interest. If I have to go through the slices, however, I would need to draw a different size rectangle on each slice. This would be challenging, but would also make it difficult to compare between samples. Is there any way to define a ROI in one plane and have it generate the appropriate ROIs down through my stack? thanks, mike

[justin.senseney]

Mooseo,

I understand what you are looking for, something like http://pacific.mpi-cbg.de/BinaryInterpolator.java is what you have specifically asked for.  It might also be worth it to see if the 3D project tool can do what you need in Image->Stacks->3D Project...  I was thinking you could set your lower and upper transparency bounds to be the intensity range for the out-of-plane object.  Then for some slice of the projection, your object would appear in-plane (you will need to increase your slice spacing to see it).  The 3D Viewer might also have a clipping plane option, this would also do what you need if it exists.

-Justin Senseney
________________________________________
From: mooseo [[hidden email]]
Sent: Tuesday, May 14, 2013 2:10 PM
To: List IMAGEJ
Subject: ROI across slices

I'm trying to do a simple analysis of density across a stack of ct images.
Unfortunately, my ROI is simple to define in one plane, but challenging in
the plane in which the volume is sliced. Essentially, I want a cylinder that
goes through my object.If I rotate my object in the volume viewer, I can
draw a circle around my region of interest. If I have to go through the
slices, however, I would need to draw a different size rectangle on each
slice. This would be challenging, but would also make it difficult to
compare between samples.Is there any way to define a ROI in one plane and
have it generate the appropriate ROIs down through my stack?thanks,mike



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[dscho]

Hi,

On Tue, 14 May 2013, Senseney, Justin (NIH/CIT) [G] wrote:

> I understand what you are looking for, something like
> http://pacific.mpi-cbg.de/BinaryInterpolator.java is what you have
> specifically asked for.

Please note that the correct URL is http://fiji.sc/BinaryInterpolator.java
since the machine that was pacific.mpi-cbg.de died (it has been replaced
since, but it is not up-to-date because I did not get around to set it up
as a mirror of the new fiji.sc machine).

Ciao,
Dscho

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[Michael Doube-4]

Hi,

> Is there any way to define a ROI in one plane and
> have it generate the appropriate ROIs down through my stack?

With help from Johannes some time ago, BoneJ wrapped up the
BinaryInterpolator and makes the ROIs for every slice and puts them in
the ROI manager, given hand-drawn ROIs on, say, every 10th or 20th slice
of your image.

Install BoneJ and you get a new command called 'Interpolate ROIs' under
Plugins > Stacks.

http://bonej.org/

Michael
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[mooseo]

Thank you very much to everyone who responded. It looks like the 3D project tool can do what I need. I appreciate the help.

cheers,
moose