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 |
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 |
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, Predoc
labs of Prof. Damian Brunner Institute of Molecular Life Sciences and Prof. Ohad Medalia Institute of Biochemistry University of Zuerich |
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