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Re: how to encode an.avi readable by ImageJ

Posted by Yann BOURSIAC on Feb 12, 2010; 3:30pm
URL: http://imagej.273.s1.nabble.com/how-to-encode-an-avi-readable-by-ImageJ-tp3689341p3689347.html

Thanks for your reply,

@Arttu: since my recordings are 2-4h long, converting the video into
images sequences is pretty heavy

@Curtis: LOCI  uses mainly the AVIreader built in the last versions of
ImageJ and has many restrictions in the format:
"Only a few formats are supported:

    *
          o Uncompressed 8 bit with palette (LUT)
          o Uncompressed 8 & 16 bit grayscale
          o Uncompressed 24 & 32 bit RGB (alpha channel ignored)
          o Uncompressed 32 bit AYUV (alpha channel ignored)
          o Various YUV 4:2:2 compressed formats
          o PNG or JPEG-encoded individual frames. Note that most MJPG
            (motion-JPEG) formats are not read correctly.
    * Does not read AVI formats with more than one frame per chunk
    * Palette changes during the video not supported
    * Out-of-sequence frames (sequence given by index) not supported
    * Different frame sizes in one file (rcFrame) not supported
    * Conversion of (A)YUV formats to grayscale is non-standard"

So my problem now is to encode in a compatible format, which I was not
able to do so far in VLC or virtualdubmod, am I using the wrong codecs?

Here is a link to a blank 1min video in the recorded format
http://dl.free.fr/vWm0MGO2l



Thanks

Yann

Arttu Miettinen a écrit :

> Hi Yann,
>
> As a temporary workaround, maybe you could export your .avi files to image
> sequences which ImageJ can easily handle? VirtualDub should be able to do
> this if it can open your .avi.
>
> - Arttu Miettinen
>
>
>
>  
>> Hi Yann,
>>
>> Did you try using the Bio-Formats plugin?
>>   http://www.loci.wisc.edu/bio-formats/imagej
>>
>> If it doesn't work, we would need a link to an example AVI file, to
>> investigate the problem further.
>>
>> -Curtis
>>
>> On Fri, Feb 5, 2010 at 10:23 AM, Yann BOURSIAC <[hidden email]>
>> wrote:
>>    
>>> Hi all,
>>>
>>> ImageJ has the possibility to open .avi files. However, when I try, I
>>> get
>>> the error message "cannot open video files missing Huffman tables".
>>> So my question is: how can I encode my files (coming from a DVD
>>> recorder)
>>> into an avi that will be readable by ImageJ?
>>> I tried some codecs from VLC or virtualdub but never succeeded.
>>>
>>> Alternatively, the final aim is to measure the diameter of a round cell
>>> along time. Our setup include a microscope camera linked to a DVD
>>> recorder.
>>> I would like to use an equivalent of the ruler tool from ImageJ. Do you
>>> know
>>> any possibility or any other alternative?
>>>
>>> Thank You
>>>
>>> Yann
>>>
>>>      
>
>