[ome-users] Problematic OME-TIFF file

[Brian Loranger]

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
> _______________________________________________
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> ome-users at lists.openmicroscopy.org.uk
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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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