TransformJ Update

[Erik Meijering]

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

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[Jan Eglinger]

Dear Erik,

thank you for the update, it looks promising!
Did you also make changes in imagescience itself concerning anisotropic
image handling? Your huge commit on github [1] mixes cosmetic changes
with meaningful code changes, so it is a little hard to grasp what
actually changed.
It would be great if you could shortly comment on that.

Regards,
Jan

[1]:
https://github.com/fiji/imagescience/commit/46f778a29d7097d9b6f785484a5be7dc048a4718


On 22.08.2015 11:53, Erik Meijering 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
>

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[Erik Meijering]

Dear Jan,

The actual algorithms are all in the imagescience library, so, yes, that's
where the real changes are. The TransformJ plugin classes are basically
just interfaces to the imagescience algorithms.

If you want more information on the changes, please consult the release
notes of the different projects on my website:

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

Best,

Erik

> Dear Erik,
>
> thank you for the update, it looks promising!
> Did you also make changes in imagescience itself concerning anisotropic
> image handling? Your huge commit on github [1] mixes cosmetic changes
> with meaningful code changes, so it is a little hard to grasp what
> actually changed.
> It would be great if you could shortly comment on that.
>
> Regards,
> Jan
>
> [1]:
> https://github.com/fiji/imagescience/commit/46f778a29d7097d9b6f785484a5be7dc048a4718
>
>
> On 22.08.2015 11:53, Erik Meijering 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
>>
>
>

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

[lechristophe]

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

[Mark Hiner]

>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

[lechristophe]

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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