Open Microscopy Environment

Hi

I am very new to omero. I have managed to upgrade the omero to 4.4.1 with the instruction from the site. The installation went smoothly and now I am testing the functionality.

I have imported jp2 files to omero and after the import, the message said "failed to create thumpnail" and I cant seem to view those images from omero(via web and via insight webstart) also.
Is there any log or anything that I could check the problem? Is there anything that I missed out during installation to see those jp2 files? I tried with normal jpg files and they seems fine.

If my way of describing the problem is not clear enough, please let me know.

How large (in X and Y) is the JP2 file?

hi

one of the files is 26673x21201 in dimensions and 67.9MB in size.

thanks and regards,

Okay, based on how the JPEG-2000 file is tiled it may not be possible for OMERO or Bio-Formats to decode it without at least 26673 * 21201 (539MB) of heap space allocated to PixelData-0. OMERO works with completely uncompressed data. Would you be willing to give us the file for testing?

Hi cxallan

Thank you for the reply. We could send you the files. Please let me have your email address to send you the link to download.

thanks again.

regards,

File uploading instructions sent in a private message.

Hi
May I know if there is any update?
thanks.

Thank you for sending files, and my apologies for not responding right away.

I was able to duplicate the problem with the .jp2 files, and so have filed a ticket on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/9544

You also sent an .ndpi file, which is known to be poorly supported as documented in this ticket:

http://trac.openmicroscopy.org.uk/ome/ticket/5092

thanks.