3D Viewer- Animation's transparency when rotating

[mduenas]

Hello all,

I'm currently using 3D Viewer and I'm having trouble visualizing the animation of my object. When my object rotates, the animation goes transparent in some sections (here I'm able to see the internal layers) and opaque in others. Is there a way to have the animation just be were it goes transparent, rather than flashing back and forth?

Thank you,

Maria

[ctrueden]

Hi Maria,

> When my object rotates, the animation goes transparent in some
> sections (here I'm able to see the internal layers) and opaque in
> others.

The differences in transparency are an artifact of how the 3D Viewer
generates its volume visualization. It is actually a series of
semi-transparent slices oriented at the closest angle to "top down" from
the camera. You can see this most dramatically if you:

A) visualize an image stack with very few slices, such as the Mitosis sample
B) orient the volume at an edge or corner, then rotate back and forth
across the border

One way to minimize the discrepancy is to use the Reslice command with
smaller output spacing, and "Avoid interpolation" unchecked. As a rule of
thumb: the closer your Z resolution is to your X and Y resolution, the less
of a discrepancy there will be.

You could also try other 3D visualization solutions with your data, such as
the BigDataViewer [1], Volume Viewer [2], or Icy [3].

Regards,
Curtis

[1] http://imagej.net/BigDataViewer
[2] http://imagej.net/Volume_Viewer
[3] http://imagej.net/Icy


On Tue, Jun 30, 2015 at 9:43 AM, mduenas <[hidden email]> wrote:

> Hello all,
>
> I'm currently using 3D Viewer and I'm having trouble visualizing the
> animation of my object. When my object rotates, the animation goes
> transparent in some sections (here I'm able to see the internal layers) and
> opaque in others. Is there a way to have the animation just be were it goes
> transparent, rather than flashing back and forth?
>
> Thank you,
>
> Maria
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/3D-Viewer-Animation-s-transparency-when-rotating-tp5013360.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Doube-4]

Hi Maria,

On 30/06/15 17:22, Curtis Rueden wrote:
> You could also try other 3D visualization solutions with your data, such as
> the BigDataViewer [1], Volume Viewer [2], or Icy [3].

For a cross-platform open-source solution, you might like to try Drishti:

https://github.com/AjayLimaye/drishti
https://github.com/AjayLimaye/drishti/releases
http://nci.org.au/systems-services/scientific-visualisation/visualisation-services/

It's biased towards CT and X-ray microtomography datasets.

Best regards,

Michael



<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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[cromatina]

Hi guys!

I have the same problem of Maria. My segmented areas look transparent in
some regions depending on the angle of visualization. I have not been able
to apply Reslice command to make the spacing between stacks smaller. Could
someone help me to find Reslice command, please?

Thanks!

2015-06-30 18:11 GMT+02:00 Curtis Rueden <[hidden email]>:

> Hi Maria,
>
> > When my object rotates, the animation goes transparent in some
> > sections (here I'm able to see the internal layers) and opaque in
> > others.
>
> The differences in transparency are an artifact of how the 3D Viewer
> generates its volume visualization. It is actually a series of
> semi-transparent slices oriented at the closest angle to "top down" from
> the camera. You can see this most dramatically if you:
>
> A) visualize an image stack with very few slices, such as the Mitosis
> sample
> B) orient the volume at an edge or corner, then rotate back and forth
> across the border
>
> One way to minimize the discrepancy is to use the Reslice command with
> smaller output spacing, and "Avoid interpolation" unchecked. As a rule of
> thumb: the closer your Z resolution is to your X and Y resolution, the less
> of a discrepancy there will be.
>
> You could also try other 3D visualization solutions with your data, such as
> the BigDataViewer [1], Volume Viewer [2], or Icy [3].
>
> Regards,
> Curtis
>
> [1] http://imagej.net/BigDataViewer
> [2] http://imagej.net/Volume_Viewer
> [3] http://imagej.net/Icy
>
>
> On Tue, Jun 30, 2015 at 9:43 AM, mduenas <[hidden email]> wrote:
>
> > Hello all,
> >
> > I'm currently using 3D Viewer and I'm having trouble visualizing the
> > animation of my object. When my object rotates, the animation goes
> > transparent in some sections (here I'm able to see the internal layers)
> and
> > opaque in others. Is there a way to have the animation just be were it
> goes
> > transparent, rather than flashing back and forth?
> >
> > Thank you,
> >
> > Maria
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/3D-Viewer-Animation-s-transparency-when-rotating-tp5013360.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Ignacio Arganda-Carreras-2]

Image > Stack > Reslice

In general, if you press the key "L", the Command Finder will pop up and
there you can type any command you want.

Cheers!

On Wed, Jul 8, 2015 at 2:04 PM, Andrea Chicano <[hidden email]>
wrote:

> Hi guys!
>
> I have the same problem of Maria. My segmented areas look transparent in
> some regions depending on the angle of visualization. I have not been able
> to apply Reslice command to make the spacing between stacks smaller. Could
> someone help me to find Reslice command, please?
>
> Thanks!
>
> 2015-06-30 18:11 GMT+02:00 Curtis Rueden <[hidden email]>:
>
> > Hi Maria,
> >
> > > When my object rotates, the animation goes transparent in some
> > > sections (here I'm able to see the internal layers) and opaque in
> > > others.
> >
> > The differences in transparency are an artifact of how the 3D Viewer
> > generates its volume visualization. It is actually a series of
> > semi-transparent slices oriented at the closest angle to "top down" from
> > the camera. You can see this most dramatically if you:
> >
> > A) visualize an image stack with very few slices, such as the Mitosis
> > sample
> > B) orient the volume at an edge or corner, then rotate back and forth
> > across the border
> >
> > One way to minimize the discrepancy is to use the Reslice command with
> > smaller output spacing, and "Avoid interpolation" unchecked. As a rule of
> > thumb: the closer your Z resolution is to your X and Y resolution, the
> less
> > of a discrepancy there will be.
> >
> > You could also try other 3D visualization solutions with your data, such
> as
> > the BigDataViewer [1], Volume Viewer [2], or Icy [3].
> >
> > Regards,
> > Curtis
> >
> > [1] http://imagej.net/BigDataViewer
> > [2] http://imagej.net/Volume_Viewer
> > [3] http://imagej.net/Icy
> >
> >
> > On Tue, Jun 30, 2015 at 9:43 AM, mduenas <[hidden email]> wrote:
> >
> > > Hello all,
> > >
> > > I'm currently using 3D Viewer and I'm having trouble visualizing the
> > > animation of my object. When my object rotates, the animation goes
> > > transparent in some sections (here I'm able to see the internal layers)
> > and
> > > opaque in others. Is there a way to have the animation just be were it
> > goes
> > > transparent, rather than flashing back and forth?
> > >
> > > Thank you,
> > >
> > > Maria
> > >
> > >
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://imagej.1557.x6.nabble.com/3D-Viewer-Animation-s-transparency-when-rotating-tp5013360.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > --
> > > 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
>

--
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 : [phone] - fax : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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[cromatina]

Thank you! That worked! Now I wonder if there is the possibility to draw
shadows in the segmented structures. I would like to apply shadows in the
inner zones just to have tridimensional effect when I show a snapshot of
the volume. Do you know if this is possible? Thanks!

Best,

Andrea

2015-07-09 10:42 GMT+02:00 Ignacio Arganda-Carreras <
[hidden email]>:

> Image > Stack > Reslice
>
> In general, if you press the key "L", the Command Finder will pop up and
> there you can type any command you want.
>
> Cheers!
>
> On Wed, Jul 8, 2015 at 2:04 PM, Andrea Chicano <[hidden email]>
> wrote:
>
> > Hi guys!
> >
> > I have the same problem of Maria. My segmented areas look transparent in
> > some regions depending on the angle of visualization. I have not been
> able
> > to apply Reslice command to make the spacing between stacks smaller.
> Could
> > someone help me to find Reslice command, please?
> >
> > Thanks!
> >
> > 2015-06-30 18:11 GMT+02:00 Curtis Rueden <[hidden email]>:
> >
> > > Hi Maria,
> > >
> > > > When my object rotates, the animation goes transparent in some
> > > > sections (here I'm able to see the internal layers) and opaque in
> > > > others.
> > >
> > > The differences in transparency are an artifact of how the 3D Viewer
> > > generates its volume visualization. It is actually a series of
> > > semi-transparent slices oriented at the closest angle to "top down"
> from
> > > the camera. You can see this most dramatically if you:
> > >
> > > A) visualize an image stack with very few slices, such as the Mitosis
> > > sample
> > > B) orient the volume at an edge or corner, then rotate back and forth
> > > across the border
> > >
> > > One way to minimize the discrepancy is to use the Reslice command with
> > > smaller output spacing, and "Avoid interpolation" unchecked. As a rule
> of
> > > thumb: the closer your Z resolution is to your X and Y resolution, the
> > less
> > > of a discrepancy there will be.
> > >
> > > You could also try other 3D visualization solutions with your data,
> such
> > as
> > > the BigDataViewer [1], Volume Viewer [2], or Icy [3].
> > >
> > > Regards,
> > > Curtis
> > >
> > > [1] http://imagej.net/BigDataViewer
> > > [2] http://imagej.net/Volume_Viewer
> > > [3] http://imagej.net/Icy
> > >
> > >
> > > On Tue, Jun 30, 2015 at 9:43 AM, mduenas <[hidden email]> wrote:
> > >
> > > > Hello all,
> > > >
> > > > I'm currently using 3D Viewer and I'm having trouble visualizing the
> > > > animation of my object. When my object rotates, the animation goes
> > > > transparent in some sections (here I'm able to see the internal
> layers)
> > > and
> > > > opaque in others. Is there a way to have the animation just be were
> it
> > > goes
> > > > transparent, rather than flashing back and forth?
> > > >
> > > > Thank you,
> > > >
> > > > Maria
> > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > > >
> > >
> >
> http://imagej.1557.x6.nabble.com/3D-Viewer-Animation-s-transparency-when-rotating-tp5013360.html
> > > > Sent from the ImageJ mailing list archive at Nabble.com.
> > > >
> > > > --
> > > > 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
> >
>
>
>
> --
> 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 : [phone] - fax : [phone]
> 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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