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3D Viewer plugin time lapse

Knecht, David
We have tried to use 3D Viewer to render a time lapse dataset.  The manual says it should work, and when the hyper stack is opened, there is a first time point box, but you can’t change that from 0 and it only renders the first z stack of the time series.  Has anyone gotten this to work?  Thanks- Dave

Dr. David Knecht
Professor , Department of Molecular and Cell Biology
University of Connecticut
91 N. Eagleville Rd.
U-3125
Storrs, CT 06269-3125
860-486-2200


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Re: 3D Viewer plugin time lapse

qian chen
The 3D viewer does work for us with both Z- and time-series rendered. Ours
is ImageJ 1.51g with Java 1.6.0_20.
Best,
Qian

Qian Chen, Ph.D.
Assistant Professor
University of Toledo
Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
Ohio 43606

Office: Wolfe Hall RM4267
Phone: 419-530-1593 <(419)%20530-1593>https://qian-chen-gdrc.squarespace.com/


On Wed, Apr 26, 2017 at 2:05 PM, qian chen <[hidden email]> wrote:

> The 3D viewer does work for us with both Z- and time-series rendered. Ours
> is ImageJ 1.51g with Java 1.6.0_20.
> Best,
> Qian
>
> Qian Chen, Ph.D.
> Assistant Professor
> University of Toledo
> Department of Biological Sciences, MS: 6012801 West Bancroft STToledo, Ohio 43606
>
> Office: Wolfe Hall RM4267
> Phone: 419-530-1593 <(419)%20530-1593>https://qian-chen-gdrc.squarespace.com/
>
>
> On Wed, Apr 26, 2017 at 12:05 PM, Knecht, David <[hidden email]>
> wrote:
>
>> We have tried to use 3D Viewer to render a time lapse dataset.  The
>> manual says it should work, and when the hyper stack is opened, there is a
>> first time point box, but you can’t change that from 0 and it only renders
>> the first z stack of the time series.  Has anyone gotten this to work?
>> Thanks- Dave
>>
>> Dr. David Knecht
>> Professor , Department of Molecular and Cell Biology
>> University of Connecticut
>> 91 N. Eagleville Rd.
>> U-3125
>> Storrs, CT 06269-3125
>> 860-486-2200
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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Re: 3D Viewer plugin time lapse

Knecht, David
Thanks for the reply.  I tried it in ImageJ and it worked perfectly after it upgraded its Java3D.  But it still doesn’t work in Fiji.  I have contacted the Fiji developers to let them know.  Dave

Dr. David Knecht
Professor , Department of Molecular and Cell Biology
University of Connecticut
91 N. Eagleville Rd.
U-3125
Storrs, CT 06269-3125
860-486-2200

> On Apr 26, 2017, at 2:10 PM, qian chen <[hidden email]> wrote:
>
> The 3D viewer does work for us with both Z- and time-series rendered. Ours
> is ImageJ 1.51g with Java 1.6.0_20.
> Best,
> Qian
>
> Qian Chen, Ph.D.
> Assistant Professor
> University of Toledo
> Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
> Ohio 43606
>
> Office: Wolfe Hall RM4267
> Phone: 419-530-1593 <(419)%20530-1593>https://qian-chen-gdrc.squarespace.com/
>
>
> On Wed, Apr 26, 2017 at 2:05 PM, qian chen <[hidden email]> wrote:
>
>> The 3D viewer does work for us with both Z- and time-series rendered. Ours
>> is ImageJ 1.51g with Java 1.6.0_20.
>> Best,
>> Qian
>>
>> Qian Chen, Ph.D.
>> Assistant Professor
>> University of Toledo
>> Department of Biological Sciences, MS: 6012801 West Bancroft STToledo, Ohio 43606
>>
>> Office: Wolfe Hall RM4267
>> Phone: 419-530-1593 <(419)%20530-1593>https://qian-chen-gdrc.squarespace.com/
>>
>>
>> On Wed, Apr 26, 2017 at 12:05 PM, Knecht, David <[hidden email]>
>> wrote:
>>
>>> We have tried to use 3D Viewer to render a time lapse dataset.  The
>>> manual says it should work, and when the hyper stack is opened, there is a
>>> first time point box, but you can’t change that from 0 and it only renders
>>> the first z stack of the time series.  Has anyone gotten this to work?
>>> Thanks- Dave
>>>
>>> Dr. David Knecht
>>> Professor , Department of Molecular and Cell Biology
>>> University of Connecticut
>>> 91 N. Eagleville Rd.
>>> U-3125
>>> Storrs, CT 06269-3125
>>> 860-486-2200
>>>
>>>
>>> --
>>> 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: 3D Viewer plugin time lapse

ctrueden
Hi Dave,

> I tried it in ImageJ and it worked perfectly after it upgraded its
> Java3D.  But it still doesn’t work in Fiji.  I have contacted the Fiji
> developers to let them know.

It is an issue with Java 8 vs. Java 6, and therefore Java 3D 1.6 vs. Java
3D 1.5.

There are some technical details here:
https://imagej.net/Java_8#About_Java_3D

If you want it to work in Fiji, then please download a Life-Line version of
Fiji from:
    https://imagej.net/Fiji/Downloads#Life-Line_Fiji_versions

These old versions of Fiji ship with Java 6, and should behave similarly to
how the 3D Viewer behaves in plain ImageJ 1.x.

Regards,
Curtis

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


On Wed, Apr 26, 2017 at 3:59 PM, Knecht, David <[hidden email]>
wrote:

> Thanks for the reply.  I tried it in ImageJ and it worked perfectly after
> it upgraded its Java3D.  But it still doesn’t work in Fiji.  I have
> contacted the Fiji developers to let them know.  Dave
>
> Dr. David Knecht
> Professor , Department of Molecular and Cell Biology
> University of Connecticut
> 91 N. Eagleville Rd.
> U-3125
> Storrs, CT 06269-3125
> 860-486-2200
>
> > On Apr 26, 2017, at 2:10 PM, qian chen <[hidden email]> wrote:
> >
> > The 3D viewer does work for us with both Z- and time-series rendered.
> Ours
> > is ImageJ 1.51g with Java 1.6.0_20.
> > Best,
> > Qian
> >
> > Qian Chen, Ph.D.
> > Assistant Professor
> > University of Toledo
> > Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
> > Ohio 43606
> >
> > Office: Wolfe Hall RM4267
> > Phone: 419-530-1593 <(419)%20530-1593>https://
> qian-chen-gdrc.squarespace.com/
> >
> >
> > On Wed, Apr 26, 2017 at 2:05 PM, qian chen <[hidden email]> wrote:
> >
> >> The 3D viewer does work for us with both Z- and time-series rendered.
> Ours
> >> is ImageJ 1.51g with Java 1.6.0_20.
> >> Best,
> >> Qian
> >>
> >> Qian Chen, Ph.D.
> >> Assistant Professor
> >> University of Toledo
> >> Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
> Ohio 43606
> >>
> >> Office: Wolfe Hall RM4267
> >> Phone: 419-530-1593 <(419)%20530-1593>https://
> qian-chen-gdrc.squarespace.com/
> >>
> >>
> >> On Wed, Apr 26, 2017 at 12:05 PM, Knecht, David <[hidden email]
> >
> >> wrote:
> >>
> >>> We have tried to use 3D Viewer to render a time lapse dataset.  The
> >>> manual says it should work, and when the hyper stack is opened, there
> is a
> >>> first time point box, but you can’t change that from 0 and it only
> renders
> >>> the first z stack of the time series.  Has anyone gotten this to work?
> >>> Thanks- Dave
> >>>
> >>> Dr. David Knecht
> >>> Professor , Department of Molecular and Cell Biology
> >>> University of Connecticut
> >>> 91 N. Eagleville Rd.
> >>> U-3125
> >>> Storrs, CT 06269-3125
> >>> 860-486-2200
> >>>
> >>>
> >>> --
> >>> 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: 3D Viewer plugin time lapse

gankaku
Hi David, Hi Curtis,

I run the newest Fiji (ImageJ 2.0.0-rc-59/1.51n; Java 1.8.0_66 [64-bit];
Windows 10) with the Java 8 update site enabled. Here, the 3D display and
time series display of the 5D Mitosis sample works perfectly for me in the
3D Viewer.
It contains the following Java 3D files in the jar folder:

j3dcore-1.6.0-scijava-2.jar
j3dutils-1.6.0-scijava-2.jar

So I guess it is also running Java 3D version 1.6. But I never manually
upgraded any Java3D files. Potentially, connected additionally, I also have
the 3D Suite update site enabled and I am not sure if this is automatically
fetching the Java3D 1.6 as needed?

Hope this helps further in getting closer to a solution.

Kind regards,
Jan

2017-05-11 21:50 GMT+02:00 Curtis Rueden <[hidden email]>:

> Hi Dave,
>
> > I tried it in ImageJ and it worked perfectly after it upgraded its
> > Java3D.  But it still doesn’t work in Fiji.  I have contacted the Fiji
> > developers to let them know.
>
> It is an issue with Java 8 vs. Java 6, and therefore Java 3D 1.6 vs. Java
> 3D 1.5.
>
> There are some technical details here:
> https://imagej.net/Java_8#About_Java_3D
>
> If you want it to work in Fiji, then please download a Life-Line version of
> Fiji from:
>     https://imagej.net/Fiji/Downloads#Life-Line_Fiji_versions
>
> These old versions of Fiji ship with Java 6, and should behave similarly to
> how the 3D Viewer behaves in plain ImageJ 1.x.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Apr 26, 2017 at 3:59 PM, Knecht, David <[hidden email]>
> wrote:
>
> > Thanks for the reply.  I tried it in ImageJ and it worked perfectly after
> > it upgraded its Java3D.  But it still doesn’t work in Fiji.  I have
> > contacted the Fiji developers to let them know.  Dave
> >
> > Dr. David Knecht
> > Professor , Department of Molecular and Cell Biology
> > University of Connecticut
> > 91 N. Eagleville Rd.
> > U-3125
> > Storrs, CT 06269-3125
> > 860-486-2200
> >
> > > On Apr 26, 2017, at 2:10 PM, qian chen <[hidden email]> wrote:
> > >
> > > The 3D viewer does work for us with both Z- and time-series rendered.
> > Ours
> > > is ImageJ 1.51g with Java 1.6.0_20.
> > > Best,
> > > Qian
> > >
> > > Qian Chen, Ph.D.
> > > Assistant Professor
> > > University of Toledo
> > > Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
> > > Ohio 43606
> > >
> > > Office: Wolfe Hall RM4267
> > > Phone: 419-530-1593 <(419)%20530-1593>https://
> > qian-chen-gdrc.squarespace.com/
> > >
> > >
> > > On Wed, Apr 26, 2017 at 2:05 PM, qian chen <[hidden email]>
> wrote:
> > >
> > >> The 3D viewer does work for us with both Z- and time-series rendered.
> > Ours
> > >> is ImageJ 1.51g with Java 1.6.0_20.
> > >> Best,
> > >> Qian
> > >>
> > >> Qian Chen, Ph.D.
> > >> Assistant Professor
> > >> University of Toledo
> > >> Department of Biological Sciences, MS: 6012801 West Bancroft STToledo,
> > Ohio 43606
> > >>
> > >> Office: Wolfe Hall RM4267
> > >> Phone: 419-530-1593 <(419)%20530-1593>https://
> > qian-chen-gdrc.squarespace.com/
> > >>
> > >>
> > >> On Wed, Apr 26, 2017 at 12:05 PM, Knecht, David <
> [hidden email]
> > >
> > >> wrote:
> > >>
> > >>> We have tried to use 3D Viewer to render a time lapse dataset.  The
> > >>> manual says it should work, and when the hyper stack is opened, there
> > is a
> > >>> first time point box, but you can’t change that from 0 and it only
> > renders
> > >>> the first z stack of the time series.  Has anyone gotten this to
> work?
> > >>> Thanks- Dave
> > >>>
> > >>> Dr. David Knecht
> > >>> Professor , Department of Molecular and Cell Biology
> > >>> University of Connecticut
> > >>> 91 N. Eagleville Rd.
> > >>> U-3125
> > >>> Storrs, CT 06269-3125
> > >>> 860-486-2200
> > >>>
> > >>>
> > >>> --
> > >>> 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



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