[ome-users] Large SVS file convertion problem

[Melissa Linkert]

Hi,

> Lately, I am using the Bio-Formats/bfconvert to convert SVS to JPEG.
> Some of the SVS files are really big and I got the follow exception:
> 
> Exception in thread "main" loci.formats.FormatException: Image plane
> too large. Only 2GB of data can be extracted at one time. You can
> workaround the problem by opening the plane in tiles; for further
> details, see: http://www.openmicroscopy.org/site/support/faq/bio-formats/i-see-an-outofmemory-or-negativearraysize-error-message-when-attempting-to-open-an-svs-or-jpeg-2000-file.-what-does-this-mean
> 
> Is there any easy solution for this problem? Do I have to crop a large
> image into smaller pieces first? Is there any way to stitch them
> together after converting?

Bio-Formats does not support saving images with more than 2 GB of pixel
data into a single JPEG file.  You will need to save smaller tiles into
separate JPEG files, like this:

  $ bfconvert -crop 0,0,4096,4096 input.svs output.jpg

where '0,0,4096,4096' is the X coordinate, Y coordinate, width, and
height of the tile to be saved.

However, you could convert to an OME-TIFF file (with or without JPEG
compression) instead, and then there is no need to save individual tiles or
stitch them back together.  This command should save the entire image
into a single file (with JPEG compression):

  $ bfconvert -compression JPEG input.svs output.ome.tiff

Regards,
-Melissa

On Thu, Oct 25, 2012 at 03:26:12PM -0400, Jianjiong Gao wrote:
> Hello,
> 
> First of all, thanks for maintaining such a great resource!
> 
> Lately, I am using the Bio-Formats/bfconvert to convert SVS to JPEG.
> Some of the SVS files are really big and I got the follow exception:
> 
> Exception in thread "main" loci.formats.FormatException: Image plane
> too large. Only 2GB of data can be extracted at one time. You can
> workaround the problem by opening the plane in tiles; for further
> details, see: http://www.openmicroscopy.org/site/support/faq/bio-formats/i-see-an-outofmemory-or-negativearraysize-error-message-when-attempting-to-open-an-svs-or-jpeg-2000-file.-what-does-this-mean
> 
> Is there any easy solution for this problem? Do I have to crop a large
> image into smaller pieces first? Is there any way to stitch them
> together after converting?
> 
> Thank you!
> -JJ
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