Reslice (project) at arbitrary angle in a 3D stack

[lechristophe]

Hi,

What is available now in ImageJ/Fiji for maoking projections along an
arbitrary x,y,z direction in a 3D stack? I found some discussions circa
2009 mentioning VisBio from C. Rueden, but I'm wondering if there is
something more recent and integrated in ImageJ/Fiji (via 3D viewer maybe?)

Christophe

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

On Jun 18, 2015, at 14:27, Christophe Leterrier wrote:

> What is available now in ImageJ/Fiji for maoking projections along an
> arbitrary x,y,z direction in a 3D stack? I found some discussions circa
> 2009 mentioning VisBio from C. Rueden, but I'm wondering if there is
> something more recent and integrated in ImageJ/Fiji (via 3D viewer maybe?)

Hi Christophe,

you can rotate a stack in x/y by Image>Transform>Rotate, then exchange x and z (or y and z) by Image>Stacks>Reslice, and rotate again. This should allow you to have you any arbitrary slice direction. It won't be 3D-interactive however.

Michael

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Saalfeld, Stephan]

Hey Christophe,

if you want to interactively slice it in arbotrary orientations, you
should use BigDataViewer

http://fiji.sc/BigDataViewer

if you need a z-projection along an arbitrary axis, you can use
BigDataViewer's predecessor

http://fiji.sc/Interactive_Stack_Rotation

interactively rotate the stack and then press ENTER which renders the
full stack in this orientation.  You can then use z-projection as usual.

Both plugins are the standard distribution of Fiji.

Best,
Stephan



On Thu, 2015-06-18 at 14:51 +0200, Michael Schmid wrote:

> On Jun 18, 2015, at 14:27, Christophe Leterrier wrote:
>
> > What is available now in ImageJ/Fiji for maoking projections along an
> > arbitrary x,y,z direction in a 3D stack? I found some discussions circa
> > 2009 mentioning VisBio from C. Rueden, but I'm wondering if there is
> > something more recent and integrated in ImageJ/Fiji (via 3D viewer maybe?)
>
> Hi Christophe,
>
> you can rotate a stack in x/y by Image>Transform>Rotate, then exchange x and z (or y and z) by Image>Stacks>Reslice, and rotate again. This should allow you to have you any arbitrary slice direction. It won't be 3D-interactive however.
>
> Michael
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html