trakem2 save aligned tif images as movie

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trakem2 save aligned tif images as movie

mandue
Hello everyone.

I have some trouble using the trakem2 plugin.

I used it to align tifs of serial sections.
I now want to save this as a movie sequence (I do not care about the file format) but cannot find a way to do so...
Also, I would be very thankful if one of you could give me a tip on how to crop all the aligned images in one go.
And another question (sorry, I am completely new to this program :P ): if I want to change the rotation of all the aligned images in one go, how best to do it?

Thank you very much for your replies!  !!!
cheers,
mandy
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Re: trakem2 save aligned tif images as movie

Stephan Saalfeld
Hi Mandy,

you right click the canvas, do

Export -> Make Flat Image

Choose the scale and background color of your series and either show or
save it as a series of tiff files.  You can then use Fiji/ImageJ to
convert this stack into an avi container that would play in most
players.  Or you use avconv/ffmpeg if you want to be fancy ;), e.g.:

avconv -r 20 -i %04d.tif -f mov -vcodec libx264 -b 9600k movie.mov

Generates a 20fps h.264-compressed movie at ~9600k bitrate in a
quicktime mov container from a series of tif files that are numbered

0000.tif
0001.tif
0002.tif ...

Best,
Stephan



On Thu, 2013-11-14 at 09:26 -0800, mandue wrote:

> Hello everyone.
>
> I have some trouble using the trakem2 plugin.
>
> I used it to align tifs of serial sections.
> I now want to save this as a movie sequence (I do not care about the file
> format) but cannot find a way to do so...
> Also, I would be very thankful if one of you could give me a tip on how to
> crop all the aligned images in one go.
> And another question (sorry, I am completely new to this program :P ): if I
> want to change the rotation of all the aligned images in one go, how best to
> do it?
>
> Thank you very much for your replies!  !!!
> cheers,
> mandy
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/trakem2-save-aligned-tif-images-as-movie-tp5005565.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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Re: trakem2 save aligned tif images as movie

mandue
Hej hej Stephan,

thanks a lot for the reply - and it was fast, don`t worry.
It worked perfectly fine exporting it now, I really enjoy the TrakEM2 plugin - if one knows some tricks. ;)

Best wishes,
Mandy



On 19.11.2013, at 13:11, Stephan Saalfeld [via ImageJ] wrote:

Hi Mandy,

you right click the canvas, do

Export -> Make Flat Image

Choose the scale and background color of your series and either show or
save it as a series of tiff files.  You can then use Fiji/ImageJ to
convert this stack into an avi container that would play in most
players.  Or you use avconv/ffmpeg if you want to be fancy ;), e.g.:

avconv -r 20 -i %04d.tif -f mov -vcodec libx264 -b 9600k movie.mov

Generates a 20fps h.264-compressed movie at ~9600k bitrate in a
quicktime mov container from a series of tif files that are numbered

0000.tif
0001.tif
0002.tif ...

Best,
Stephan



On Thu, 2013-11-14 at 09:26 -0800, mandue wrote:

> Hello everyone.
>
> I have some trouble using the trakem2 plugin.
>
> I used it to align tifs of serial sections.
> I now want to save this as a movie sequence (I do not care about the file
> format) but cannot find a way to do so...
> Also, I would be very thankful if one of you could give me a tip on how to
> crop all the aligned images in one go.
> And another question (sorry, I am completely new to this program :P ): if I
> want to change the rotation of all the aligned images in one go, how best to
> do it?
>
> Thank you very much for your replies!  !!!
> cheers,
> mandy
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/trakem2-save-aligned-tif-images-as-movie-tp5005565.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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