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cromatina

3D Viewer:

Dear ImageJ list,

I am using 3D viewer to see my original 3D reconstruction together with my
segmented structures (.labels). But I am not able to move these two
selections together...Someone knows how can I overlap my original volume
with segmented areas?

My aim is to be able to take snapshot of some slices showing the original
structures and also the original volume showing coloured structures
(segmented).

Best regards,

Andrea

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

Ignacio Arganda-Carreras-2

Re: 3D Viewer:

Dear Andrea,

I think what you need to do is to load the two volumes (original image and
labels) separately in ImageJ/Fiji and then call the 3D viewer. That way you
can add them both to the viewer and visualize them together, change the
transparency of the labels, etc.

Best,

ignacio

On Thu, Jun 25, 2015 at 11:59 AM, Andrea Chicano <[hidden email]>
wrote:

> Dear ImageJ list,
>
> I am using 3D viewer to see my original 3D reconstruction together with my
> segmented structures (.labels). But I am not able to move these two
> selections together...Someone knows how can I overlap my original volume
> with segmented areas?
>
> My aim is to be able to take snapshot of some slices showing the original
> structures and also the original volume showing coloured structures
> (segmented).
>
> Best regards,
>
> Andrea
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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

cromatina

Re: 3D Viewer:

Dear Ignacio,

I think I'm doing what you said: I open my original stack of images, and
also import > amira my .labels. Then I go to the plugins and call 3D
viewer. I think that when it opens, the two selections (original and
labels) show the same slice, but when I try to move them, it only moves one
of the selections...

I've tried to select both of them in Edit > Select but I can't...well, I
could once, but I've not been able to move them together anymore...

Suggestions are very welcome!

Best,
Andrea

2015-06-25 12:08 GMT+02:00 Ignacio Arganda-Carreras <
[hidden email]>:

> Dear Andrea,
>
> I think what you need to do is to load the two volumes (original image and
> labels) separately in ImageJ/Fiji and then call the 3D viewer. That way you
> can add them both to the viewer and visualize them together, change the
> transparency of the labels, etc.
>
> Best,
>
> ignacio
>
> On Thu, Jun 25, 2015 at 11:59 AM, Andrea Chicano <[hidden email]
> >
> wrote:
>
> > Dear ImageJ list,
> >
> > I am using 3D viewer to see my original 3D reconstruction together with
> my
> > segmented structures (.labels). But I am not able to move these two
> > selections together...Someone knows how can I overlap my original volume
> > with segmented areas?
> >
> > My aim is to be able to take snapshot of some slices showing the original
> > structures and also the original volume showing coloured structures
> > (segmented).
> >
> > Best regards,
> >
> > Andrea
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> Website: http://sites.google.com/site/iargandacarreras/
> <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Ignacio Arganda-Carreras-2

Re: 3D Viewer:

I see. If you don't select any of them, then you can change the view around
them (move, rotate, etc).

Is that what you want?

On Thu, Jun 25, 2015 at 12:22 PM, Andrea Chicano <[hidden email]>
wrote:

> Dear Ignacio,
>
> I think I'm doing what you said: I open my original stack of images, and
> also import > amira my .labels. Then I go to the plugins and call 3D
> viewer. I think that when it opens, the two selections (original and
> labels) show the same slice, but when I try to move them, it only moves one
> of the selections...
>
> I've tried to select both of them in Edit > Select but I can't...well, I
> could once, but I've not been able to move them together anymore...
>
> Suggestions are very welcome!
>
> Best,
> Andrea
>
> 2015-06-25 12:08 GMT+02:00 Ignacio Arganda-Carreras <
> [hidden email]>:
>
> > Dear Andrea,
> >
> > I think what you need to do is to load the two volumes (original image
> and
> > labels) separately in ImageJ/Fiji and then call the 3D viewer. That way
> you
> > can add them both to the viewer and visualize them together, change the
> > transparency of the labels, etc.
> >
> > Best,
> >
> > ignacio
> >
> > On Thu, Jun 25, 2015 at 11:59 AM, Andrea Chicano <
> [hidden email]
> > >
> > wrote:
> >
> > > Dear ImageJ list,
> > >
> > > I am using 3D viewer to see my original 3D reconstruction together with
> > my
> > > segmented structures (.labels). But I am not able to move these two
> > > selections together...Someone knows how can I overlap my original
> volume
> > > with segmented areas?
> > >
> > > My aim is to be able to take snapshot of some slices showing the
> original
> > > structures and also the original volume showing coloured structures
> > > (segmented).
> > >
> > > Best regards,
> > >
> > > Andrea
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> > Bâtiment 2
> > INRA Centre de Versailles-Grignon
> > Route de St-Cyr (RD10)
> > 78026 Versailles Cedex France
> >
> > Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> > Website: http://sites.google.com/site/iargandacarreras/
> > <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

gankaku

Re: 3D Viewer:

In reply to this post by cromatina

Dear Andrea,

if you add more than one reconstruction mesh and you accidentally rotate
one against another you can reset this movement with >Edit >Transformation
> Reset Transform and then you can fix the reconstruction with >Edit
>Transformation >Lock.

If you do this for all the reconstructions you have in your viewer window
you can align them and disable independent movements.

Hope this helps.
Kind regards,

Jan

Am 25.06.2015 05:24 schrieb "Andrea Chicano" <[hidden email]>:

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

cromatina

Re: 3D Viewer:

In reply to this post by Ignacio Arganda-Carreras-2

Thanks a lot guys! You've helped me a lot! I was wasting a lot of time
trying to do something properly! The Edit > Transformation > Lock option
helped me to fix both of the stacks in the same position. And at the moment
(with your help) I have a movie with my results and segmented structures!!!

Best regards,

Andrea

2015-06-25 12:30 GMT+02:00 Ignacio Arganda-Carreras <
[hidden email]>:

> I see. If you don't select any of them, then you can change the view around
> them (move, rotate, etc).
>
> Is that what you want?
>
> On Thu, Jun 25, 2015 at 12:22 PM, Andrea Chicano <[hidden email]
> >
> wrote:
>
> > Dear Ignacio,
> >
> > I think I'm doing what you said: I open my original stack of images, and
> > also import > amira my .labels. Then I go to the plugins and call 3D
> > viewer. I think that when it opens, the two selections (original and
> > labels) show the same slice, but when I try to move them, it only moves
> one
> > of the selections...
> >
> > I've tried to select both of them in Edit > Select but I can't...well, I
> > could once, but I've not been able to move them together anymore...
> >
> > Suggestions are very welcome!
> >
> > Best,
> > Andrea
> >
> > 2015-06-25 12:08 GMT+02:00 Ignacio Arganda-Carreras <
> > [hidden email]>:
> >
> > > Dear Andrea,
> > >
> > > I think what you need to do is to load the two volumes (original image
> > and
> > > labels) separately in ImageJ/Fiji and then call the 3D viewer. That way
> > you
> > > can add them both to the viewer and visualize them together, change the
> > > transparency of the labels, etc.
> > >
> > > Best,
> > >
> > > ignacio
> > >
> > > On Thu, Jun 25, 2015 at 11:59 AM, Andrea Chicano <
> > [hidden email]
> > > >
> > > wrote:
> > >
> > > > Dear ImageJ list,
> > > >
> > > > I am using 3D viewer to see my original 3D reconstruction together
> with
> > > my
> > > > segmented structures (.labels). But I am not able to move these two
> > > > selections together...Someone knows how can I overlap my original
> > volume
> > > > with segmented areas?
> > > >
> > > > My aim is to be able to take snapshot of some slices showing the
> > original
> > > > structures and also the original volume showing coloured structures
> > > > (segmented).
> > > >
> > > > Best regards,
> > > >
> > > > Andrea
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > >
> > >
> > > --
> > > Ignacio Arganda-Carreras, Ph.D.
> > > Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> > > Bâtiment 2
> > > INRA Centre de Versailles-Grignon
> > > Route de St-Cyr (RD10)
> > > 78026 Versailles Cedex France
> > >
> > > Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> > > Website: http://sites.google.com/site/iargandacarreras/
> > > <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> Website: http://sites.google.com/site/iargandacarreras/
> <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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