how to encode an.avi readable by ImageJ

[Yann BOURSIAC]

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

[ctrueden]

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
>

[Arttu Miettinen]

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
>>
>

[Yann BOURSIAC]

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
>>>
>>>      
>
>  

[Michael Schmid]

Hi Everyone,

is the problem of "missing Huffman tables" a frequent one?

If there are many reports about such problems it might be worthwhile  
to add code to fix this problem, but I don't know common JPEG-
encoded .AVI files (aka M-JPEG encoded) without Huffman tables are.  
In principle, such a fix would be possible (it would not help to read  
MPEG-encoded files, however; MPEG is a rather complex encoding).

For those interested in details: (M-)JPEG encoded video files do not  
need to supply Huffman tables in the individual frames, but many (M-)
JPEG-encoded video files include them nonetheless. Currently ImageJ  
can only decode those (M-)JPEG-encoded video files that include  
Huffman tables.


Michael
________________________________________________________________

On 5 Feb 2010, at 17:23, Yann BOURSIAC 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

[Yann BOURSIAC]

Hi all,
I finally got my problem solved, but not exactly what I wanted.

The procedure that works for me is to encode the video files into a .mov
file and using the quicktime plugin. The  file can then be open with
ImageJ, although it's taking quite a while for big files on my computer.

Yann

Michael Schmid a écrit :

> Hi Everyone,
>
> is the problem of "missing Huffman tables" a frequent one?
>
> If there are many reports about such problems it might be worthwhile
> to add code to fix this problem, but I don't know common JPEG-encoded
> .AVI files (aka M-JPEG encoded) without Huffman tables are. In
> principle, such a fix would be possible (it would not help to read
> MPEG-encoded files, however; MPEG is a rather complex encoding).
>
> For those interested in details: (M-)JPEG encoded video files do not
> need to supply Huffman tables in the individual frames, but many
> (M-)JPEG-encoded video files include them nonetheless. Currently
> ImageJ can only decode those (M-)JPEG-encoded video files that include
> Huffman tables.
>
>
> Michael
> ________________________________________________________________
>
> On 5 Feb 2010, at 17:23, Yann BOURSIAC 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
>

[Michael Schmid]

Hi Yann,

up to now I got no other mail saying that video files without Huffman  
tables  would be a problem, so I think it is not worthwhile adding  
this to ImageJ. After all, one of the big advantages of ImageJ is its  
small size, which makes it start very quickly. Thus, and also to keep  
the code readable, there is some consensus in the ImageJ community  
not to add code that would be rarely used.

When converting to Quicktime, make sure that there are no bad  
compression artifacts! To avoid compression artifacts, usually it  
would be preferable to  convert it into an uncompressed or mildly  
compressed format like YUY2, but this creates very large files that  
may exceed the maximum size of AVI1 of 2GB (ImageJ can't read AVI2  
aka OpenDML, but if I remember correctly there was a post on this  
mailing list some time ago on a plugin capable of reading AVI2).

On Windows, you could also have a look at AviSynth - it has the  
possibility to read video files of quite a few formats. You cannot  
feed AviSync directly as an input into ImageJ, but you would again  
have to use VirtualDub for writing the converted file. In VirtualDub,  
instead of the .avi file you have to open the AviSynt Script (.avs);  
the .avs file opens the avi file. AviSynth can convert to e.g. RGB24  
or YUY2 format readable by ImageJ (use ConvertToRGB24 or  
ConvertToYUY2 in your AviSynth script).
Of course, this does not solve the problem of the 2 GB file size  
limit of AVI1 after conversion.


Michael
________________________________________________________________

On 18 Feb 2010, at 08:43, Yann BOURSIAC wrote:

> Hi all,
> I finally got my problem solved, but not exactly what I wanted.
>
> The procedure that works for me is to encode the video files into  
> a .mov file and using the quicktime plugin. The  file can then be  
> open with ImageJ, although it's taking quite a while for big files  
> on my computer.
>
> Yann
>
> Michael Schmid a écrit :
>> Hi Everyone,
>>
>> is the problem of "missing Huffman tables" a frequent one?
>>
>> If there are many reports about such problems it might be  
>> worthwhile to add code to fix this problem, but I don't know  
>> common JPEG-encoded .AVI files (aka M-JPEG encoded) without  
>> Huffman tables are. In principle, such a fix would be possible (it  
>> would not help to read MPEG-encoded files, however; MPEG is a  
>> rather complex encoding).
>>
>> For those interested in details: (M-)JPEG encoded video files do  
>> not need to supply Huffman tables in the individual frames, but  
>> many (M-)JPEG-encoded video files include them nonetheless.  
>> Currently ImageJ can only decode those (M-)JPEG-encoded video  
>> files that include Huffman tables.
>>
>>
>> Michael
>> ________________________________________________________________
>>
>> On 5 Feb 2010, at 17:23, Yann BOURSIAC 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
>>