[ome-users] Problematic OME-TIFF file

[Woodbridge, Mark R]

multi-image-pixels.ome.tif submitted as QA Bug | 1008.

From: Jason Swedlow [mailto:jason at lifesci.dundee.ac.uk]
Sent: 22 October 2009 23:58
To: Woodbridge, Mark R
Cc: David Gutman; ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Problematic OME-TIFF file

Hi All-

Thanks for this feedback.

>From our experience, this size should cause a problem.  In our testing, we imported multi-plane OME-TIFF's that were much larger, with no problem.

The best bet is to use qa.openmicroscopy.org.uk, and we'll take a look at the file.

Cheers,

Jason


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 from http://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.

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



--
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<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk<mailto:jason at lifesci.dundee.ac.uk>

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20091023/b454d5e4/attachment.html>