grid stitching with fiji

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grid stitching with fiji

fabrice senger-2
Dera all I try to use the grid stitching plugin in FIJI but don't want to
move in Z.
Therefore I use the provided script as provided :

mpicbg.stitching.GlobalOptimization.ignoreZ = true;

but the log window gives me an exception :

[WARNING] Ignoring unsupported output: result [java.lang.Boolean]

and if I proceed anyway with stitching there's always some movement in z.

Any suggestions ?

Thank you,

Fabrice.

I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.

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Re: grid stitching with fiji

ctrueden
Hi Fabrice,

> [WARNING] Ignoring unsupported output: result [java.lang.Boolean]

This warning comes from the SciJava script framework -- part of ImageJ2. It
means that the last computation of your script produced an array of values,
which the system wants to display, but doesn't know how. It is harmless and
can be safely ignored; it has nothing to do with stitching.

> if I proceed anyway with stitching there's always some movement in z.

Maybe if you ask on the ImageJ forum and mention the author
(@StephanPreibisch), he will comment on it?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <[hidden email]>
wrote:

> Dera all I try to use the grid stitching plugin in FIJI but don't want to
> move in Z.
> Therefore I use the provided script as provided :
>
> mpicbg.stitching.GlobalOptimization.ignoreZ = true;
>
> but the log window gives me an exception :
>
> [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>
> and if I proceed anyway with stitching there's always some movement in z.
>
> Any suggestions ?
>
> Thank you,
>
> Fabrice.
>
> I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: grid stitching with fiji

fabrice senger-2
thank you Curtis,

I will contact him directly,
Best,

Fabrice.

2016-04-26 19:02 GMT+02:00 Curtis Rueden <[hidden email]>:

> Hi Fabrice,
>
> > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>
> This warning comes from the SciJava script framework -- part of ImageJ2. It
> means that the last computation of your script produced an array of values,
> which the system wants to display, but doesn't know how. It is harmless and
> can be safely ignored; it has nothing to do with stitching.
>
> > if I proceed anyway with stitching there's always some movement in z.
>
> Maybe if you ask on the ImageJ forum and mention the author
> (@StephanPreibisch), he will comment on it?
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <[hidden email]
> >
> wrote:
>
> > Dera all I try to use the grid stitching plugin in FIJI but don't want to
> > move in Z.
> > Therefore I use the provided script as provided :
> >
> > mpicbg.stitching.GlobalOptimization.ignoreZ = true;
> >
> > but the log window gives me an exception :
> >
> > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> >
> > and if I proceed anyway with stitching there's always some movement in z.
> >
> > Any suggestions ?
> >
> > Thank you,
> >
> > Fabrice.
> >
> > I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: grid stitching with fiji

ctrueden
Hi Fabrice,

> I will contact him directly,

I encourage you to use public communication channels whenever possible.
There are others (e.g. here at LOCI) who know some things about that
plugin, and we may be able to chime in with assistance. But not if you use
private mail.

Regarding the movement in Z, this issue sounds vaguely familiar, and I
thought Stephan even commented on it once, but off the top of my head I
cannot remember any additional details. And I don't have time to dig into
the archives thoroughly right now...

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Apr 26, 2016 at 3:57 PM, Fabrice Senger <[hidden email]>
wrote:

> thank you Curtis,
>
> I will contact him directly,
> Best,
>
> Fabrice.
>
> 2016-04-26 19:02 GMT+02:00 Curtis Rueden <[hidden email]>:
>
> > Hi Fabrice,
> >
> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> >
> > This warning comes from the SciJava script framework -- part of ImageJ2.
> It
> > means that the last computation of your script produced an array of
> values,
> > which the system wants to display, but doesn't know how. It is harmless
> and
> > can be safely ignored; it has nothing to do with stitching.
> >
> > > if I proceed anyway with stitching there's always some movement in z.
> >
> > Maybe if you ask on the ImageJ forum and mention the author
> > (@StephanPreibisch), he will comment on it?
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - http://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <
> [hidden email]
> > >
> > wrote:
> >
> > > Dera all I try to use the grid stitching plugin in FIJI but don't want
> to
> > > move in Z.
> > > Therefore I use the provided script as provided :
> > >
> > > mpicbg.stitching.GlobalOptimization.ignoreZ = true;
> > >
> > > but the log window gives me an exception :
> > >
> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> > >
> > > and if I proceed anyway with stitching there's always some movement in
> z.
> > >
> > > Any suggestions ?
> > >
> > > Thank you,
> > >
> > > Fabrice.
> > >
> > > I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
> > >
> > > --
> > > 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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Re: grid stitching with fiji

Stephan Preibisch
Hi Fabrice, yes, there is fix for that. See here on the documentation page: http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z

Hope this helps,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email] <mailto:[hidden email]>
web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>

> On 26 Apr 2016, at 23:25, Curtis Rueden <[hidden email]> wrote:
>
> Hi Fabrice,
>
> > I will contact him directly,
>
> I encourage you to use public communication channels whenever possible. There are others (e.g. here at LOCI) who know some things about that plugin, and we may be able to chime in with assistance. But not if you use private mail.
>
> Regarding the movement in Z, this issue sounds vaguely familiar, and I thought Stephan even commented on it once, but off the top of my head I cannot remember any additional details. And I don't have time to dig into the archives thoroughly right now...
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software <http://loci.wisc.edu/software>
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden <http://imagej.net/User:Rueden>
> Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
>
>
> On Tue, Apr 26, 2016 at 3:57 PM, Fabrice Senger <[hidden email] <mailto:[hidden email]>> wrote:
> thank you Curtis,
>
> I will contact him directly,
> Best,
>
> Fabrice.
>
> 2016-04-26 19:02 GMT+02:00 Curtis Rueden <[hidden email] <mailto:[hidden email]>>:
>
> > Hi Fabrice,
> >
> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> >
> > This warning comes from the SciJava script framework -- part of ImageJ2. It
> > means that the last computation of your script produced an array of values,
> > which the system wants to display, but doesn't know how. It is harmless and
> > can be safely ignored; it has nothing to do with stitching.
> >
> > > if I proceed anyway with stitching there's always some movement in z.
> >
> > Maybe if you ask on the ImageJ forum and mention the author
> > (@StephanPreibisch), he will comment on it?
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - http://loci.wisc.edu/software <http://loci.wisc.edu/software>
> > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden <http://imagej.net/User:Rueden>
> > Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
> >
> >
> > On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <[hidden email] <mailto:[hidden email]>
> > >
> > wrote:
> >
> > > Dera all I try to use the grid stitching plugin in FIJI but don't want to
> > > move in Z.
> > > Therefore I use the provided script as provided :
> > >
> > > mpicbg.stitching.GlobalOptimization.ignoreZ = true;
> > >
> > > but the log window gives me an exception :
> > >
> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
> > >
> > > and if I proceed anyway with stitching there's always some movement in z.
> > >
> > > Any suggestions ?
> > >
> > > Thank you,
> > >
> > > Fabrice.
> > >
> > > I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>


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Re: grid stitching with fiji

ctrueden
Hi Stephan,

Thanks for the reply. From his first email though, it sounds like Fabrice
is already using that line:

   mpicbg.stitching.GlobalOptimization.ignoreZ = true;

And it is not working as expected... any suggestions for debugging it?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Apr 27, 2016 at 9:21 AM, Stephan Preibisch <[hidden email]>
wrote:

> Hi Fabrice, yes, there is fix for that. See here on the documentation
> page:
> http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z
>
> Hope this helps,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> Group Leader
>
> Berlin Institute of Medical Systems Biology of the MDC
> Building 89, 1.08b
>
> email: [hidden email]
> web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>
>
> On 26 Apr 2016, at 23:25, Curtis Rueden <[hidden email]> wrote:
>
> Hi Fabrice,
>
> > I will contact him directly,
>
> I encourage you to use public communication channels whenever possible.
> There are others (e.g. here at LOCI) who know some things about that
> plugin, and we may be able to chime in with assistance. But not if you use
> private mail.
>
> Regarding the movement in Z, this issue sounds vaguely familiar, and I
> thought Stephan even commented on it once, but off the top of my head I
> cannot remember any additional details. And I don't have time to dig into
> the archives thoroughly right now...
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Tue, Apr 26, 2016 at 3:57 PM, Fabrice Senger <[hidden email]>
> wrote:
>
>> thank you Curtis,
>>
>> I will contact him directly,
>> Best,
>>
>> Fabrice.
>>
>> 2016-04-26 19:02 GMT+02:00 Curtis Rueden <[hidden email]>:
>>
>> > Hi Fabrice,
>> >
>> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>> >
>> > This warning comes from the SciJava script framework -- part of
>> ImageJ2. It
>> > means that the last computation of your script produced an array of
>> values,
>> > which the system wants to display, but doesn't know how. It is harmless
>> and
>> > can be safely ignored; it has nothing to do with stitching.
>> >
>> > > if I proceed anyway with stitching there's always some movement in z.
>> >
>> > Maybe if you ask on the ImageJ forum and mention the author
>> > (@StephanPreibisch), he will comment on it?
>> >
>> > Regards,
>> > Curtis
>> >
>> > --
>> > Curtis Rueden
>> > LOCI software architect - http://loci.wisc.edu/software
>> > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
>> > Did you know ImageJ has a forum? http://forum.imagej.net/
>> >
>> >
>> > On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <
>> [hidden email]
>> > >
>> > wrote:
>> >
>> > > Dera all I try to use the grid stitching plugin in FIJI but don't
>> want to
>> > > move in Z.
>> > > Therefore I use the provided script as provided :
>> > >
>> > > mpicbg.stitching.GlobalOptimization.ignoreZ = true;
>> > >
>> > > but the log window gives me an exception :
>> > >
>> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>> > >
>> > > and if I proceed anyway with stitching there's always some movement
>> in z.
>> > >
>> > > Any suggestions ?
>> > >
>> > > Thank you,
>> > >
>> > > Fabrice.
>> > >
>> > > I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
>> > >
>> > > --
>> > > 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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Re: grid stitching with fiji

Stephan Preibisch
Hi,

the ImageJ log and then a minimal example for reproducing it would be helpful. But as this worked before, and it is a pretty simple hack, I would rather bet on a typo or something like that at this point.

Cheers,
Stephan


> On 27 Apr 2016, at 16:46, Curtis Rueden <[hidden email]> wrote:
>
> Hi Stephan,
>
> Thanks for the reply. From his first email though, it sounds like Fabrice is already using that line:
>
>    mpicbg.stitching.GlobalOptimization.ignoreZ = true;
>
> And it is not working as expected... any suggestions for debugging it?
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software <http://loci.wisc.edu/software>
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden <http://imagej.net/User:Rueden>
> Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
>
>
> On Wed, Apr 27, 2016 at 9:21 AM, Stephan Preibisch <[hidden email] <mailto:[hidden email]>> wrote:
> Hi Fabrice, yes, there is fix for that. See here on the documentation page: http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z <http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z>
>
> Hope this helps,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> Group Leader
>
> Berlin Institute of Medical Systems Biology of the MDC
> Building 89, 1.08b
>
> email: [hidden email] <mailto:[hidden email]>
> web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>
>
>> On 26 Apr 2016, at 23:25, Curtis Rueden <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> Hi Fabrice,
>>
>> > I will contact him directly,
>>
>> I encourage you to use public communication channels whenever possible. There are others (e.g. here at LOCI) who know some things about that plugin, and we may be able to chime in with assistance. But not if you use private mail.
>>
>> Regarding the movement in Z, this issue sounds vaguely familiar, and I thought Stephan even commented on it once, but off the top of my head I cannot remember any additional details. And I don't have time to dig into the archives thoroughly right now...
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - http://loci.wisc.edu/software <http://loci.wisc.edu/software>
>> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden <http://imagej.net/User:Rueden>
>> Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
>>
>>
>> On Tue, Apr 26, 2016 at 3:57 PM, Fabrice Senger <[hidden email] <mailto:[hidden email]>> wrote:
>> thank you Curtis,
>>
>> I will contact him directly,
>> Best,
>>
>> Fabrice.
>>
>> 2016-04-26 19:02 GMT+02:00 Curtis Rueden <[hidden email] <mailto:[hidden email]>>:
>>
>> > Hi Fabrice,
>> >
>> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>> >
>> > This warning comes from the SciJava script framework -- part of ImageJ2. It
>> > means that the last computation of your script produced an array of values,
>> > which the system wants to display, but doesn't know how. It is harmless and
>> > can be safely ignored; it has nothing to do with stitching.
>> >
>> > > if I proceed anyway with stitching there's always some movement in z.
>> >
>> > Maybe if you ask on the ImageJ forum and mention the author
>> > (@StephanPreibisch), he will comment on it?
>> >
>> > Regards,
>> > Curtis
>> >
>> > --
>> > Curtis Rueden
>> > LOCI software architect - http://loci.wisc.edu/software <http://loci.wisc.edu/software>
>> > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden <http://imagej.net/User:Rueden>
>> > Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
>> >
>> >
>> > On Wed, Mar 30, 2016 at 10:21 AM, Fabrice Senger <[hidden email] <mailto:[hidden email]>
>> > >
>> > wrote:
>> >
>> > > Dera all I try to use the grid stitching plugin in FIJI but don't want to
>> > > move in Z.
>> > > Therefore I use the provided script as provided :
>> > >
>> > > mpicbg.stitching.GlobalOptimization.ignoreZ = true;
>> > >
>> > > but the log window gives me an exception :
>> > >
>> > > [WARNING] Ignoring unsupported output: result [java.lang.Boolean]
>> > >
>> > > and if I proceed anyway with stitching there's always some movement in z.
>> > >
>> > > Any suggestions ?
>> > >
>> > > Thank you,
>> > >
>> > > Fabrice.
>> > >
>> > > I run Fiji imageJ2.0.0-rc-43/1.50g; java 1.6.0_65 on a mac.
>> > >
>> > > --
>> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>> > >
>> >
>> > --
>> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>> >
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>>
>
>


--
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