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Re: TransformJ Update

Posted by lechristophe on Aug 26, 2015; 2:57pm
URL: http://imagej.273.s1.nabble.com/TransformJ-Update-tp5014108p5014158.html

Just got it via the updater, thanks!

Christophe

On Wed, Aug 26, 2015 at 4:22 PM, Mark Hiner <[hidden email]> wrote:

> >Is the update supposed to be automatically included in Fiji?
>
>
> I just uploaded these releases. The new versions should all be available
> through the updater now! Let us know if there are any problems.
>
> Best,
> Mark
>
> On Wed, Aug 26, 2015 at 5:11 AM, Christophe Leterrier <
> [hidden email]> wrote:
>
> > Hi,
> >
> > Is the update supposed to be automatically included in Fiji? I see that
> the
> > IJ updater still does not install it (my imagscience is still 2.5.0).
> >
> > I saw that an update to NeuronJ is available and necessary for the new
> > imagescience.jar, so I have to be sure which version I'm using.
> >
> > Thanks,
> >
> > Christophe
> >
> > On Sat, Aug 22, 2015 at 11:53 AM, Erik Meijering <
> > [hidden email]
> > > wrote:
> >
> > > Dear TransformJ users,
> > >
> > > TransformJ 4.0.0 is now available (
> > > http://www.imagescience.org/meijering/software/transformj/) for ImageJ
> > > users and will soon also appear in the Fiji distribution.
> > >
> > > It is a long-awaited major update. So long, in fact, that in the
> meantime
> > > many of you probably got used to the shortcomings of the package and
> > found
> > > ways to work around them. Needless to say these work-arounds will no
> > longer
> > > work with the new version, so you may need to update your code/macros a
> > bit.
> > >
> > > Apart from some cosmetic changes the most important fundamental change
> is
> > > that the Affine and Rotate plugins are now able to properly work with
> > image
> > > stacks having anisotropic voxels. This means you no longer need to
> first
> > > resample your data to isotropic voxels (if this was part of your
> pipeline
> > > you will need to remove that step). The plugins offer the possibility
> to
> > > either sample the transformed image on the same grid (same anisotropy)
> as
> > > the input image (this is the default mode) or to resample the stack
> > > isotropically while transforming (an option to be selected by the
> user).
> > >
> > > Even though this means TransformJ now finally works the way it should
> > have
> > > from the beginning, perhaps some of you would like to keep the old
> > behavior
> > > of the plugins. This is possible. The only thing you need to do then is
> > > temporarily set the voxel width/height/depth to 1.0 (which is what
> > > TransformJ has been assuming all along previously), then perform the
> > > transformation, and afterwards put these properties back to their old
> > > values.
> > >
> > > For consistency with the Affine plugin (the most generic plugin of the
> > > package), two other changes were introduced. First, the Scale plugin by
> > > default no longer rescales the voxel properties in order to retain the
> > > physical image dimensions, but this is now an option (to be selected by
> > the
> > > user). Second, the Translate plugin now assumes the translation
> distances
> > > to be in physical units (determined by the voxel properties), but an
> > option
> > > has been added (to be selected by the user) to take these distances as
> > > voxel units.
> > >
> > > Have fun transforming your data!
> > >
> > > Erik
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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