Plugin for a zooming movie

[Heerpa]

Hi everyone,

I have huge images (~10k x 10k pixels), and for a presentation, I wouldlike
to show this high resolution. So my idea is to make a movie of zooming out
of a fine structure, eventually showing the whole image. As I did not find a
plugin for that in a quick search, I wouldlike to ask you guys whether you
are arware of such a plugin before I write one..

Thanks
   Heinrich

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[Stephan Saalfeld]

Hi Heinrich,

I once wrote one for zooming into a TrakEM2 section series:

https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/trakem2_zoom_movie.bsh

You could drag your image into a new TrakEM2 project, in Fiji

File > New > TrakEM2 (blank)

than drag your big image into the canvas.  Then open the script in
Fiji's scripting interpreter (it is written in Beanshell), modify line
44 to

layer = layer.getParent().getLayer( 0 );

to not move through the stack since you do not have one.  Then, you can
modify the parameters such as tx and ty (lines 5 and 6, the rotation
center and zoom-in target), l (the number of frames in line 9), s (in
line 57, the scale increase) and the rotation (in line 61) to your
needs.  The acceleration function is a cosine as specified in line 51.

Now select a rectangle Roi in the canvas and press the run button.

Sorry for the clumsiness of the code but it's been hacked in a rush and
serves its purpose.

Examples of an earlier version without scale bars here:

http://fly.mpi-cbg.de/~saalfeld/video/worm.mov

http://fly.mpi-cbg.de/~saalfeld/video/fly.mov

Using TrakEM2 releases you from the responsibility to take care yourself
for perfect image quality at all zoom levels.

Best,
Stephan




On Thu, 2013-02-21 at 13:19 +0100, Heinrich Grabmayr wrote:

> Hi everyone,
>
> I have huge images (~10k x 10k pixels), and for a presentation, I wouldlike
> to show this high resolution. So my idea is to make a movie of zooming out
> of a fine structure, eventually showing the whole image. As I did not find a
> plugin for that in a quick search, I wouldlike to ask you guys whether you
> are arware of such a plugin before I write one..
>
> Thanks
>    Heinrich
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Heerpa]

Hi Stephan,
thank you for that suggestion. I have never done anything with TrakEM2, so there I am a complete newbie. I tried to drag&drop my image (tif) into every part of the windows, but it would not work (mouse icon tells me it is not a valid target). Also jpegs do not work. The TrakEM manual also told me to drag and drop and did not help me any further (http://www.ini.uzh.ch/~acardona/trakem2_manual.html#fs_start_project). Is there anything else I need to watch out for? I use Fiji with all of today's updates..

best, Heinrich

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Stephan Saalfeld
Gesendet: Donnerstag, 21. Februar 2013 15:44
An: [hidden email]
Betreff: Re: Plugin for a zooming movie

Hi Heinrich,

I once wrote one for zooming into a TrakEM2 section series:

https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/trakem2_zoom_movie.bsh

You could drag your image into a new TrakEM2 project, in Fiji

File > New > TrakEM2 (blank)

than drag your big image into the canvas.  Then open the script in Fiji's scripting interpreter (it is written in Beanshell), modify line
44 to

layer = layer.getParent().getLayer( 0 );

to not move through the stack since you do not have one.  Then, you can modify the parameters such as tx and ty (lines 5 and 6, the rotation center and zoom-in target), l (the number of frames in line 9), s (in line 57, the scale increase) and the rotation (in line 61) to your needs.  The acceleration function is a cosine as specified in line 51.

Now select a rectangle Roi in the canvas and press the run button.

Sorry for the clumsiness of the code but it's been hacked in a rush and serves its purpose.

Examples of an earlier version without scale bars here:

http://fly.mpi-cbg.de/~saalfeld/video/worm.mov

http://fly.mpi-cbg.de/~saalfeld/video/fly.mov

Using TrakEM2 releases you from the responsibility to take care yourself for perfect image quality at all zoom levels.

Best,
Stephan




On Thu, 2013-02-21 at 13:19 +0100, Heinrich Grabmayr wrote:

> Hi everyone,
>
> I have huge images (~10k x 10k pixels), and for a presentation, I
> wouldlike to show this high resolution. So my idea is to make a movie
> of zooming out of a fine structure, eventually showing the whole
> image. As I did not find a plugin for that in a quick search, I
> wouldlike to ask you guys whether you are arware of such a plugin before I write one..
>
> Thanks
>    Heinrich
>
> --
> 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

[Heerpa]

Hi Stephan,

now I got it to work - I just confused the computers and where I had java3d installed.
The zoomed movie looks really cool, thanks a lot!
My image is a composite and it seems like only one channel has been imported by drag&drop. Is that so, or are the other planes hidden? Also, I can't find how to change the LUT etc...

Cheers, Heinrich

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Stephan Saalfeld
Gesendet: Donnerstag, 21. Februar 2013 15:44
An: [hidden email]
Betreff: Re: Plugin for a zooming movie

Hi Heinrich,

I once wrote one for zooming into a TrakEM2 section series:

https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/trakem2_zoom_movie.bsh

You could drag your image into a new TrakEM2 project, in Fiji

File > New > TrakEM2 (blank)

than drag your big image into the canvas.  Then open the script in Fiji's scripting interpreter (it is written in Beanshell), modify line
44 to

layer = layer.getParent().getLayer( 0 );

to not move through the stack since you do not have one.  Then, you can modify the parameters such as tx and ty (lines 5 and 6, the rotation center and zoom-in target), l (the number of frames in line 9), s (in line 57, the scale increase) and the rotation (in line 61) to your needs.  The acceleration function is a cosine as specified in line 51.

Now select a rectangle Roi in the canvas and press the run button.

Sorry for the clumsiness of the code but it's been hacked in a rush and serves its purpose.

Examples of an earlier version without scale bars here:

http://fly.mpi-cbg.de/~saalfeld/video/worm.mov

http://fly.mpi-cbg.de/~saalfeld/video/fly.mov

Using TrakEM2 releases you from the responsibility to take care yourself for perfect image quality at all zoom levels.

Best,
Stephan




On Thu, 2013-02-21 at 13:19 +0100, Heinrich Grabmayr wrote:

> Hi everyone,
>
> I have huge images (~10k x 10k pixels), and for a presentation, I
> wouldlike to show this high resolution. So my idea is to make a movie
> of zooming out of a fine structure, eventually showing the whole
> image. As I did not find a plugin for that in a quick search, I
> wouldlike to ask you guys whether you are arware of such a plugin before I write one..
>
> Thanks
>    Heinrich
>
> --
> 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

[Stephan Saalfeld]

Hi Heinrich,

cool.  Java3D is actually not involved... Howver---TrakEM2 can in
principle handle composite images but it doesn't help you importing
them.  Make your life easier and apply your favorite LUTs first, convert
the composite image to RGB and import it then into TrakEM2.  For getting
a color movie export, change line 88 to

ImagePlus.COLOR_RGB,

Best,
Stephan




On Fri, 2013-02-22 at 12:51 +0100, Heinrich Grabmayr wrote:

> Hi Stephan,
>
> now I got it to work - I just confused the computers and where I had java3d installed.
> The zoomed movie looks really cool, thanks a lot!
> My image is a composite and it seems like only one channel has been imported by drag&drop. Is that so, or are the other planes hidden? Also, I can't find how to change the LUT etc...
>
> Cheers, Heinrich
>
> -----Ursprüngliche Nachricht-----
> Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Stephan Saalfeld
> Gesendet: Donnerstag, 21. Februar 2013 15:44
> An: [hidden email]
> Betreff: Re: Plugin for a zooming movie
>
> Hi Heinrich,
>
> I once wrote one for zooming into a TrakEM2 section series:
>
> https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/trakem2_zoom_movie.bsh
>
> You could drag your image into a new TrakEM2 project, in Fiji
>
> File > New > TrakEM2 (blank)
>
> than drag your big image into the canvas.  Then open the script in Fiji's scripting interpreter (it is written in Beanshell), modify line
> 44 to
>
> layer = layer.getParent().getLayer( 0 );
>
> to not move through the stack since you do not have one.  Then, you can modify the parameters such as tx and ty (lines 5 and 6, the rotation center and zoom-in target), l (the number of frames in line 9), s (in line 57, the scale increase) and the rotation (in line 61) to your needs.  The acceleration function is a cosine as specified in line 51.
>
> Now select a rectangle Roi in the canvas and press the run button.
>
> Sorry for the clumsiness of the code but it's been hacked in a rush and serves its purpose.
>
> Examples of an earlier version without scale bars here:
>
> http://fly.mpi-cbg.de/~saalfeld/video/worm.mov
>
> http://fly.mpi-cbg.de/~saalfeld/video/fly.mov
>
> Using TrakEM2 releases you from the responsibility to take care yourself for perfect image quality at all zoom levels.
>
> Best,
> Stephan
>
>
>
>
> On Thu, 2013-02-21 at 13:19 +0100, Heinrich Grabmayr wrote:
> > Hi everyone,
> >
> > I have huge images (~10k x 10k pixels), and for a presentation, I
> > wouldlike to show this high resolution. So my idea is to make a movie
> > of zooming out of a fine structure, eventually showing the whole
> > image. As I did not find a plugin for that in a quick search, I
> > wouldlike to ask you guys whether you are arware of such a plugin before I write one..
> >
> > Thanks
> >    Heinrich
> >
> > --
> > 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

... [show rest of quote]

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