frame-by-frame processing of large stacks?

[John R. Frank-2]

Is there a way to convert a large stack into a .avi or .mov without
loading the whole thing into RAM?  Perhaps some command line call to
imagej that allows it to process it frame-by-frame?

I have multipage TIFFs that are a >1.5GB, so the 32-bit JVM limits prevent
me from making a movie from them with ImageJ's GUI.  I hope there is
another way.

Thank you for your help!

Yours,
John


--
___________________________
John R. Frank <[hidden email]>
Physics Graduate Student

[Burger Wilhelm]

John,
 
you may want to check the MovieIO package (available at my web site http://www.fh-hagenberg.at/staff/burger/imagej/index.html) for this. It allows to read or write (or both) and process video files frame by frame. It only uses a single ImageProcessor object for this task.
 
Regards,
Wilhelm

________________________________

Von: ImageJ Interest Group im Auftrag von John R. Frank
Gesendet: Di 20.11.2007 22:30
An: [hidden email]
Betreff: frame-by-frame processing of large stacks?



Is there a way to convert a large stack into a .avi or .mov without
loading the whole thing into RAM?  Perhaps some command line call to
imagej that allows it to process it frame-by-frame?

I have multipage TIFFs that are a >1.5GB, so the 32-bit JVM limits prevent
me from making a movie from them with ImageJ's GUI.  I hope there is
another way.

Thank you for your help!

Yours,
John


--
___________________________
John R. Frank <[hidden email]>
Physics Graduate Student

[ctrueden]

Hi John,

The Bio-Formats library (http://www.loci.wisc.edu/ome/formats.html)
was built around the idea of doing things plane by plane. We have a
command line tool called "bfconvert" that enables you to convert
between formats that Bio-Formats can handle, which includes conversion
of TIFF to AVI and MOV formats. This procedure is done one plane at a
time, so it takes very little memory regardless of file size.

To use the command line tools, make a new folder, download
loci_tools.jar into it, then download and extract the bftools.zip file
(from the "Using Bio-Formats from the command line" section) into that
same folder.

Then, from a Command Prompt on Windows:

cd "C:\myBioFormatsFolder"
bfconvert "C:\path\to\my.tiff" "C:\path\to\my.avi"

Or from a Terminal on Mac OS X:

cd '~/myBioFormatsFolder'
./bfconvert '/path/to/my.tiff' '/path/to/my.avi'

Please let me know if you have any questions or problems. We are also
working on a more sophisticated graphical tool for doing conversions
across multiple files, but it is not yet ready.

-Curtis

On Nov 20, 2007 3:30 PM, John R. Frank <[hidden email]> wrote:

> Is there a way to convert a large stack into a .avi or .mov without
> loading the whole thing into RAM?  Perhaps some command line call to
> imagej that allows it to process it frame-by-frame?
>
> I have multipage TIFFs that are a >1.5GB, so the 32-bit JVM limits prevent
> me from making a movie from them with ImageJ's GUI.  I hope there is
> another way.
>
> Thank you for your help!
>
> Yours,
> John
>
>
> --
> ___________________________
> John R. Frank <[hidden email]>
> Physics Graduate Student
>

[Wayne Rasband]

With ImageJ 1.39k and later, you can frame-by-frame convert a large
TIFF by opening it using File>Import>TIFF Virtual Stack and saving it
using File>Save As>AVI, File>Save As>Gif (animated GIF) or File>Save
As>QuickTime Movie. Set the frame rate in the Image>Stacks>Animation
Options dialog.

-wayne

On Nov 20, 2007, at 4:30 PM, John R. Frank wrote:

> Is there a way to convert a large stack into a .avi or .mov without
> loading the whole thing into RAM?  Perhaps some command line call to
> imagej that allows it to process it frame-by-frame?
>
> I have multipage TIFFs that are a >1.5GB, so the 32-bit JVM limits
> prevent
> me from making a movie from them with ImageJ's GUI.  I hope there is
> another way.
>
> Thank you for your help!
>
> Yours,
> John
>
>
> --
> ___________________________
> John R. Frank <[hidden email]>
> Physics Graduate Student
>