Posted by
ctrueden on
Nov 21, 2007; 6:41pm
URL: http://imagej.273.s1.nabble.com/frame-by-frame-processing-of-large-stacks-tp3697953p3697955.html
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
>