loading large files with AVI Reader

[John Soong-2]

I have ten-minute video files that are 6 GB big (thanks, Virtual Dub!) --
and I need them compressed with only intraframe compression for Ctrax. I
thought ImageJ could do this, however it only looks at the first 3350
frames (about 118 seconds) then it doesn't load any further frames. I'm not
sure if this changes with resolution or because it hits some hard 2 GB
limit. Is there a fix for it?

--
John Riemann Soong Lüwen
Biochem, Physics UVA '13

"Every difference of opinion is not a difference of principle. We have
called by different names brethren of the same principle. We are all
Republicans, we are all Federalists." -- Thomas Jefferson

We want structures that serve people, not people serving structures.
(l'Odéon, mai '68)

[Michael Schmid]

Hi John,

ImageJ should open AVI files larger than 1 or 2 GB since version 1.46c or 1.46d.
You should be aware that a large AVI needs a lot of memory, probably more than reserved for ImageJ.
Thus, you should open it as a 'virtual stack'.

If you have a new ImageJ version, it is not a memory problem, and nevertheless you can't see the full file, please turn on 'Debug mode' in Edit>Options>Misc and mail the contents of the LOG window to me, so I can have a look at it.

Michael
________________________________________________________________
On Apr 13, 2012, at 00:44, John Soong wrote:

> I have ten-minute video files that are 6 GB big (thanks, Virtual Dub!) --
> and I need them compressed with only intraframe compression for Ctrax. I
> thought ImageJ could do this, however it only looks at the first 3350
> frames (about 118 seconds) then it doesn't load any further frames. I'm not
> sure if this changes with resolution or because it hits some hard 2 GB
> limit. Is there a fix for it?
>
> --
> John Riemann Soong Lüwen
> Biochem, Physics UVA '13

[dscho]

Hi,

On Fri, 13 Apr 2012, Michael Schmid wrote:

> On Apr 13, 2012, at 00:44, John Soong wrote:
>
> > I have ten-minute video files that are 6 GB big (thanks, Virtual Dub!) --
> > and I need them compressed with only intraframe compression for Ctrax. I
> > thought ImageJ could do this, however it only looks at the first 3350
> > frames (about 118 seconds) then it doesn't load any further frames. I'm not
> > sure if this changes with resolution or because it hits some hard 2 GB
> > limit. Is there a fix for it?
>
> ImageJ should open AVI files larger than 1 or 2 GB since version 1.46c
> or 1.46d.  You should be aware that a large AVI needs a lot of memory,
> probably more than reserved for ImageJ.  Thus, you should open it as a
> 'virtual stack'.
>
> If you have a new ImageJ version, it is not a memory problem, and
> nevertheless you can't see the full file, please turn on 'Debug mode' in
> Edit>Options>Misc and mail the contents of the LOG window to me, so I
> can have a look at it.

And of course it cannot be stressed enough that there are some file format
experts who made the Bio-Formats plugin available. It is able to read
large .avi files for quite some time now. In addition, you get support for
a lot more file formats, too. Please find it here:

        http://www.loci.wisc.edu/bio-formats/

Note that to avoid the confusion some people experience with the name,
mistaking Bio-Formats for something only biologists are permitted to use,
the name will change in the near future to SCIFIO (standing for Scientific
File Input/Output).

Hth,
Johannes

[dscho]

Hi,

On Fri, 13 Apr 2012, Johannes Schindelin wrote:

> Note that to avoid the confusion some people experience with the name,
> mistaking Bio-Formats for something only biologists are permitted to use,
> the name will change in the near future to SCIFIO (standing for Scientific
> File Input/Output).

It was pointed out to me that I left the impression as if Bio-Formats
would be renamed. That is not the case.

To be clear: Bio-Formats will continue to exist. It was started primarily
as a project to support the file formats of the many microscope vendors,
to be able to read your own data back, no matter in what format it was
written. And it will continue to fulfill that mission.

However, the general framework for image I/O is so useful that it will be
available under the name "SCIFIO" with a number of general file-formats.
Bio-Formats will sit on top of it (and thereby also serve as documentation
how to plug in new formats using the SCIFIO framework).

Ciao,
Johannes