[ome-users] Problematic OME-TIFF file

[Woodbridge, Mark R]

Yes, Beta4.1 final for both server and client.

Had a closer look at the server log file when importing the ome-tiff sample from the loci webpage. Looks like an exception is occurring... could my database be corrupt? Log attached.

Mark.


From: Brian Loranger [mailto:brian.loranger at lifesci.dundee.ac.uk]
Sent: 23 October 2009 11:11
To: Woodbridge, Mark R
Cc: David Gutman; ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Problematic OME-TIFF file

Hi Mark,

Melissa and I had a look over this file this morning. The problem here is that the ome.tiff contains 2 channels, but the tiff actually only contains one. While this is a valid ome tiff, that setup is not supported in the OMERO data model (hence the reason you can open it in bio-formats but not in OMERO).

I was a bit surprised you got into a permanent analyze loop with this. I have tried importing this file on mac and windows so far and in both cases it failed 'properly' (adding the file to the QA report tab of the importer). We will probably need to provide better feedback or some workaround for both of your problem file types (the 2 to 1 channel and the multi-image-pixels ones you're having trouble with).

I'll keep trying to duplicate your endless analysis loop problem here. In the meantime can you double check for me you're using the latest server and client releases (from the download page) - just so we're all on the same page.

Thanks for the feedback Mark,

Brian

On 22 Oct 2009, at 22:26, Woodbridge, Mark R wrote:


It's about 100MB, but same problem seems to affect upload of (for example) multi-image-pixels.ome.tif fromhttp://www.loci.wisc.edu/ome/ome-tiff-data.html which is about 10MB so looks like a more general problem with some types of OME-TIFF.

But, more generally, Beta4.1 is looking good - many thanks to the OMERO developers! All our other file formats have uploaded successfully, including some which have only been supported since this new release. Other large files haven't presented a problem either.

Mark.

From: David Gutman [mailto:dagutman at gmail.com]
Sent: 22 October 2009 21:16
To: Woodbridge, Mark R
Cc: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Problematic OME-TIFF file

Mark how big is the image?  I haven't updated to the newer version of OME yet (that's next week's goal) but I would have some images work, and others die depending on file size-- often I would get an error related to ICE timing out, etc...


dg
On Thu, Oct 22, 2009 at 3:47 PM, Woodbridge, Mark R <m.woodbridge at imperial.ac.uk<mailto:m.woodbridge at imperial.ac.uk>> wrote:
Hi,

I've just been trying to upload a set of files to Beta4.1 using the importer. One file causes the Importer to get stuck in a loop where it just says 'analysing' until I cancel the import:

http://cisbic.bioinformatics.ic.ac.uk/20090422bead20x_C1.ome.tif

The importer previously refused to import the file. I'm not sure whether this was correct, as the OME-TIFF validator says it's ok, but previous investigations suggested that the channel order metadata may be wrong. Anyway, it should probably either succeed or fail rather than getting stuck ;-)

Tested with Importer running on Windows and Linux.

Mark.

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--
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine
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Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No: SC015096)

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