Unequal slice distance

[sheldon]

Hello,

Is there anybody have the experience to set unequal slice distance in imagej? As I understand, the voxel depth can only be one value but can not be changed slice by slice. Is there a solution for this? Thanks in advance!

Cheers,
Sheldon

[Saalfeld, Stephan]

ImageJ does not support non-linear calibration for spatial and temporal
axes.  You can, however, do this in TrakEM2.  As long as you need it for
reconstructing anatomy, this is probably a good idea anyways.  TrakEM2
is part of Fiji:

http://fiji.sc/wiki/index.php/TrakEM2

Best,
Stephan


On Fri, 2014-06-06 at 02:41 -0700, sheldon wrote:

> Hello,
>
> Is there anybody have the experience to set unequal slice distance in
> imagej? As I understand, the voxel depth can only be one value but can not
> be changed slice by slice. Is there a solution for this? Thanks in advance!
>
> Cheers,
> Sheldon
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Unequal-slice-distance-tp5008065.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--

Stephan Saalfeld, Ph.D.
Group Leader
Janelia Farm Research Campus
19700 Helix Drive | Ashburn, VA 20147
Phone: [phone] | Fax: [phone]
[hidden email]

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

[ctrueden]

Hi Stephan, Sheldon & everyone,

> > As I understand, the voxel depth can only be one value but can not be
> > changed slice by slice. Is there a solution for this?
>
> ImageJ does not support non-linear calibration for spatial and
> temporal axes.

ImageJ2 is designed to solve this problem (in the ImgLib2 layer) by
attaching Axis metadata to each dimension of the image. Here is a (still
theoretical) BeanShell script illustrating:

// @ImageJ ij
Dataset dataset = ij.dataset().open("/Users/curtis/data/tubhiswt.ome.tif");
 ImgPlus<?> imgPlus = dataset.getImgPlus();
int zIndex = img.dimensionIndex(Axes.Z);
CalibratedAxis originalAxis = img.axis(zIndex);
 NonlinearAxis newAxis = new DefaultNonlinearAxis(axis.type(), axis.unit(),
listOfNonlinearValues);
img.setAxis(newAxis, d);

I say "theoretical" because the NonlinearAxis & DefaultNonlinearAxis
classes do not exist yet. But we have already implemented many other sorts
of Axis, so supporting nonlinear will be very straightforward.

Note that since ImageJ2 and ImgLib2 are still in beta, these data
structures are subject to change. And of course legacy ImageJ1 plugins will
not be able to support this nonlinearity. But I just wanted to mention that
we _have_ been working on it (for over four years now!) and a solution is
on the way.

Regards,
Curtis


On Fri, Jun 6, 2014 at 8:56 AM, Stephan Saalfeld <[hidden email]
> wrote:

> ImageJ does not support non-linear calibration for spatial and temporal
> axes.  You can, however, do this in TrakEM2.  As long as you need it for
> reconstructing anatomy, this is probably a good idea anyways.  TrakEM2
> is part of Fiji:
>
> http://fiji.sc/wiki/index.php/TrakEM2
>
> Best,
> Stephan
>
>
> On Fri, 2014-06-06 at 02:41 -0700, sheldon wrote:
> > Hello,
> >
> > Is there anybody have the experience to set unequal slice distance in
> > imagej? As I understand, the voxel depth can only be one value but can
> not
> > be changed slice by slice. Is there a solution for this? Thanks in
> advance!
> >
> > Cheers,
> > Sheldon
> >
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/Unequal-slice-distance-tp5008065.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
>
> Stephan Saalfeld, Ph.D.
> Group Leader
> Janelia Farm Research Campus
> 19700 Helix Drive | Ashburn, VA 20147
> Phone: [phone] | Fax: [phone]
> [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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