file size limit

[Jeff Spector]

Hi all,
    I'm currently working on single molecule tracking at high frame
rates ( up to 1000 fps).  The camera I use records images as 16 bit
tiffs which I import as a sequence into Image J and then form an avi.
   My problem is that is seems  Image J has a limit of about 1 gig (and
seems to be more stable if that number is 768 ). This obviously limits
the size of each of my movies, and  I was wondering if there
is a way around this limitation, and if not, if anyone knows of a (free
or open source) program that will run on windows that can read 16 bit
tiffs and make large avi files ?
 Thanks in advance,
 
Jeff Spector
********************
 Purdue University      
 Department of Physics
*******************

[Wayne Rasband]

Upgrade to ImageJ 1.38q or later, import the tiff sequence as a virtual
stack, then save it as an AVI. To create a virtual stack, check "Use
Virtual Stack" in the File>Import>Image Sequence dialog.

-wayne

On May 16, 2007, at 2:30 PM, Jeff Spector wrote:

> Hi all,
>    I'm currently working on single molecule tracking at high frame
> rates ( up to 1000 fps).  The camera I use records images as 16 bit
> tiffs which I import as a sequence into Image J and then form an avi.
>   My problem is that is seems  Image J has a limit of about 1 gig (and
> seems to be more stable if that number is 768 ). This obviously limits
> the size of each of my movies, and  I was wondering if there
> is a way around this limitation, and if not, if anyone knows of a
> (free or open source) program that will run on windows that can read
> 16 bit tiffs and make large avi files ?
> Thanks in advance,
>  Jeff Spector
> ********************
> Purdue University       Department of Physics
> *******************
>

[Drizzt]

I seem to be having a similar issue going the opposite direction. I have large Avi's which I am trying to crop and then convert to Tiffs. I have been importing my Avi's as Virtual Stack, but every time the frame number is 546 (which is less than the original Avi). I presume it is a memory issue, but I was under the impression that importing as a virtual stack should take care of those kinds of issues. I too am using a High speed camera and my Avi files can get very large (larger than the available ram on my computer). Any suggestions?

Thanks,
James

[grimper]

I have also encountered the same problem. The size of uncompressed avi movie is somehow limited to 1.3g, no matter the virtual stack option was used or not. When the movie is larger than this limit, only the first frames that fits into this limit will be read and the resting frames would just be omitted. The option to select the range of frames was not working under this condition neither.

I come up with an inefficient work around: Use the ffmpeg (or other video converting tool) to convert the movie into single images and than use the import image sequence to process the movie batch by batch......

Zong

[Michael Schmid]

Hi Zong,

the problem is probably not one of file size but of AVI format: Large  
AVI files are necessarily in so-called AVI 2.0 format, but ImageJ  
interprets only AVI 1 (when inventing AVI, the Microsoft guys did not  
expect that a movie could be larger than 1 or 2 GB).  The beginning  
of an AVI 2 file is like AVI 1, but only the beginning of the movie  
can be contained there.

You could try opening your file with BioFormats, I think that it can  
also open AVI 2.

Michael
________________________________________________________________

On 1 Dec 2011, at 12:18, grimper wrote:

> I have also encountered the same problem. The size of uncompressed  
> avi movie
> is somehow limited to 1.3g, no matter the virtual stack option was  
> used or
> not. When the movie is larger than this limit, only the first  
> frames that
> fits into this limit will be read and the resting frames would just be
> omitted. The option to select the range of frames was not working  
> under this
> condition neither.
>
> I come up with an inefficient work around: Use the ffmpeg (or other  
> video
> converting tool) to convert the movie into single images and than  
> use the
> import image sequence to process the movie batch by batch......
>
> Zong

[grimper]

Hi Michael,

No success with the BioFormats(LOCI), only the first 186 frames out of 265 frames were read. The 17s movie truncated to 12 seconds.
However, if I reduce the movie size to 1/2, from 1600x1200 to 800x600, then all the 265 frames could be read. (The file size reduced from 1530mb to 381mb. ). That's why I am suspecting the size matters....

Zong

[giubi]

Hello,

Did you try to open the AVI file as virtual stack using File->Import->Using
QuickTime.

It works only on IJ 32-bit.

Cheers,
Giuseppe



On 2 December 2011 09:50, grimper <[hidden email]> wrote:

> Hi Michael,
>
> No success with the BioFormats(LOCI), only the first 186 frames out of 265
> frames were read. The 17s movie truncated to 12 seconds.
> However, if I reduce the movie size to 1/2, from 1600x1200 to 800x600, then
> all the 265 frames could be read. (The file size reduced from 1530mb to
> 381mb. ). That's why I am suspecting the size matters....
>
> Zong
>
> --
> View this message in context:
> http://imagej.588099.n2.nabble.com/file-size-limit-tp633603p7053949.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Dec 1, 2011, at 1:28 PM, Michael Schmid wrote:

> Hi Zong,
>
> the problem is probably not one of file size but of AVI format: Large  
> AVI files are necessarily in so-called AVI 2.0 format, but ImageJ  
> interprets only AVI 1 (when inventing AVI, the Microsoft guys did not  
> expect that a movie could be larger than 1 or 2 GB).  The beginning  
> of an AVI 2 file is like AVI 1, but only the beginning of the movie  
> can be contained there.
>
> You could try opening your file with BioFormats, I think that it can  
> also open AVI 2.

Thanks to Jesper Pedersen and Michael Schmid, the ImageJ 1.46c daily build supports AVI 2.0. It is also dramatically faster at opening AVIs as virtual stacks.

-wayne

> ________________________________________________________________
>
> On 1 Dec 2011, at 12:18, grimper wrote:
>
>> I have also encountered the same problem. The size of uncompressed  
>> avi movie
>> is somehow limited to 1.3g, no matter the virtual stack option was  
>> used or
>> not. When the movie is larger than this limit, only the first  
>> frames that
>> fits into this limit will be read and the resting frames would just be
>> omitted. The option to select the range of frames was not working  
>> under this
>> condition neither.
>>
>> I come up with an inefficient work around: Use the ffmpeg (or other  
>> video
>> converting tool) to convert the movie into single images and than  
>> use the
>> import image sequence to process the movie batch by batch......
>>
>> Zong