Arbitrary reslicing of a stack

[Richard Kollmar]

Dear All:

Is there a simple way to reslice an image stack in an arbitrary (not  
orthogonal) orientation with ImageJ (or other free software)?

I am trying to create isotropic uniform random (IUR) or vertical  
uniform random (VUR) sections from a TIFF stack of CT data for  
stereological surface measurements with cycloids or a vertical spatial  
grid.

Practically speaking, the orientation of my samples during acquisition  
may be random enough. Segmentation and perimeter measurements would  
also work. However, I am approaching this as a learning experience, to  
compare different methods.

One facility on our campus has Amira, but even there, arbitrary re-
slicing apparently requires scripting, and I'd like be able to do this  
in my own lab.

Thanks for any suggestions,

Richard
--
Richard Kollmar, Ph.D.
Assistant Professor
Dpt. of Molecular & Integrative Physiology and
   Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
427A Burrill Hall
407 S. Goodwin Ave., MC-114
Urbana, IL 61801
Tel. [phone]
FAX [phone]

[Stephan Saalfeld]

Hi Richard,

have a look at TransformJ

http://www.imagescience.org/meijering/software/transformj/

that does all you want. "Reslicing" is rotation + eventually mirror:

http://www.imagescience.org/meijering/software/transformj/rotate.html

http://www.imagescience.org/meijering/software/transformj/mirror.html

Best regards,
Stephan


On Tue, 2009-04-07 at 04:21 -0500, Richard Kollmar wrote:

> Dear All:
>
> Is there a simple way to reslice an image stack in an arbitrary (not  
> orthogonal) orientation with ImageJ (or other free software)?
>
> I am trying to create isotropic uniform random (IUR) or vertical  
> uniform random (VUR) sections from a TIFF stack of CT data for  
> stereological surface measurements with cycloids or a vertical
> spatial  
> grid.
>
> Practically speaking, the orientation of my samples during
> acquisition  
> may be random enough. Segmentation and perimeter measurements would  
> also work. However, I am approaching this as a learning experience,
> to  
> compare different methods.
>
> One facility on our campus has Amira, but even there, arbitrary re-
> slicing apparently requires scripting, and I'd like be able to do
> this  
> in my own lab.
>
> Thanks for any suggestions,
>
> Richard