[ome-users] aperio svs files

[Melissa Linkert]

Hi Serena,

> I can't open in Bio-formats importer svs images obtained with an Aperio
> fluorescence scanner and i would like to handle the entire image to run the
> analysis in ImageJ (actually i have to extract the image with Aperio
> software, and change the tiff format in photoshop, a little bit tricky).
> Curtis Rueden suggest me to ask for FTP server credentials to upload the
> images and understand where is the bug.

Can you please first verify that the images open if you select the "Crop
on import" option in the "Bio-Formats Import Options" window, with a
smaller subsection of the image specified (e.g. 4096x4096)?

Most .svs files contain very large images, such that opening the entire
image at once is often not possible; error messages such as
"OutOfMemoryError" or "NegativeArraySizeException" are common.  To
process these files in ImageJ, you will need to open small sections of
the image at a time.

If you are able to open small sections of the image as described above,
then there is no need to send a file - that is the expected behavior.
If you see an error message even when opening a small section of the
image, then please send the entire error message that you see, along
with a file to the FTP server sent in a private email.

Regards,
-Melissa

On Wed, Jun 26, 2013 at 03:14:09PM +0200, Serena Buscone wrote:
> Hi all,
> I can't open in Bio-formats importer svs images obtained with an Aperio
> fluorescence scanner and i would like to handle the entire image to run the
> analysis in ImageJ (actually i have to extract the image with Aperio
> software, and change the tiff format in photoshop, a little bit tricky).
> Curtis Rueden suggest me to ask for FTP server credentials to upload the
> images and understand where is the bug.
> Thanks for your help.
> Serena

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