[ome-users] Problematic OME-TIFF file

[Brian Loranger]

Hi Mark,

That's the error you should be getting from trying to import a multi- 
image-pixels ome.tif so I doubt your database has any issues. Lets try  
to delete your history database (you can use the 'wipe history' button  
on the history tab) - maybe your history file is corrupt.

Cheers,

Brian

On 23 Oct 2009, at 11:21, Woodbridge, Mark R wrote:

> 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
> 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 
> > 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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> 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)
>
> <Blitz-0.log>

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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