Problem reading avi files: Z and T variable switched?

[ashlyns]

General Questions:

Is there a way to swap the Z and T parameters of a .avi file in ImageJ.
Alternatively, can I use FFmpeg to generate an .avi file that has the appropriate Z and T parameters I need?

Background info

I am using my iPhone to take images of Drosophila larval locomotion (no budget for a camera) and would like to analyze them using a tracking plugin in Fiji/ImageJ. The original files are .mov files, which give compression errors when I try to open them directly. Simple conversion to avi files (in several different software programs including FFmpeg) does not work, as I get a slightly different compression error from ImageJ with these. I figured out that I need to change the codec of the file, so I've installed FFmpeg and borrowed some code off of this forum to generate a decompressed .avi file with a nv12 codec. The code I'm using is as follows (original file is named "test.mov):

ffmpeg –i test.mov –pix_fmt nv12 –f avi –vcodec rawvideo test2.avi

This produces an avi file that opens just fine in ImageJ through the File->Import function. the Bio-formats plugin produces unintelligible (to me) errors with these files. When I try to use these nv12 avi files with various tracking plugins (MTrack2, MTrackJ, wrMTrck) they fail to work properly. One of them (TrackMate) generates a message titled Z/T Swap? that says "It appears that you have 1 timepoint but 921 slices. Do you want to sway Z and T?". When I check the size of my image, it does indicate that I have 921 slices, which would be consistent with the problems I encounter in the tracking plugins.

Is there a way in either ImageJ or FFmpeg to switch the "Z" component of my file so that it is ready as time by these plugins? (i want 1 slice, and 921 point in time)?

I just installed and updated Fiji today (64 bit on Windows 10), so I should have the most up to date versions of everything.

Any help would be greatly appreciated!!

[Jitte Groothuis]

Dear Ashlyn,

If I understand correctly you should be able to use Image > Hyperstack >
Reorder Hyperstack... to turn your Z into T.

Good luck!
Jitte

On Thu, 8 Sep 2016 at 21:35 ashlyns <[hidden email]> wrote:

> General Questions:
>
> Is there a way to swap the Z and T parameters of a .avi file in ImageJ.
> Alternatively, can I use FFmpeg to generate an .avi file that has the
> appropriate Z and T parameters I need?
>
> Background info
>
> I am using my iPhone to take images of Drosophila larval locomotion (no
> budget for a camera) and would like to analyze them using a tracking plugin
> in Fiji/ImageJ. The original files are .mov files, which give compression
> errors when I try to open them directly. Simple conversion to avi files (in
> several different software programs including FFmpeg) does not work, as I
> get a slightly different compression error from ImageJ with these. I
> figured
> out that I need to change the codec of the file, so I've installed FFmpeg
> and borrowed some code off of this forum to generate a decompressed .avi
> file with a nv12 codec. The code I'm using is as follows (original file is
> named "test.mov):
>
> ffmpeg –i test.mov –pix_fmt nv12 –f avi –vcodec rawvideo test2.avi
>
> This produces an avi file that opens just fine in ImageJ through the
> File->Import function. the Bio-formats plugin produces unintelligible (to
> me) errors with these files. When I try to use these nv12 avi files with
> various tracking plugins (MTrack2, MTrackJ, wrMTrck) they fail to work
> properly. One of them (TrackMate) generates a message titled Z/T Swap? that
> says "It appears that you have 1 timepoint but 921 slices. Do you want to
> sway Z and T?". When I check the size of my image, it does indicate that I
> have 921 slices, which would be consistent with the problems I encounter in
> the tracking plugins.
>
> Is there a way in either ImageJ or FFmpeg to switch the "Z" component of my
> file so that it is ready as time by these plugins? (i want 1 slice, and 921
> point in time)?
>
> I just installed and updated Fiji today (64 bit on Windows 10), so I should
> have the most up to date versions of everything.
>
> Any help would be greatly appreciated!!
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Problem-reading-avi-files-Z-and-T-variable-switched-tp5017164.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[ashlyns]

That worked great! I'm thought there might be a simple solution in ImageJ, but I didn't know where to find it. Thank you!

[chin]

Hi ashlyns,

You can use either
1. Image>Hyperstacks>Stack to Hyperstacks, change number for slices(c) and frames(t)

or
2. Image>Properties, you can change slices(c), frames(t) and give the frame interval

chin