[ome-users] FW: OMERO.qa - new feedback for QA Bug

Wed Oct 12 16:47:59 BST 2016

Hi James,

We tried checking the validity of ome-xml and found that the ome-xml is invalid in this file.
This suggests that the ome-tiff was not written properly, by the acquisition software.

And if you had opened the file as Curtis suggested: then Fiji reads the file as a regular multi-page TIFF, and thus treats it as a time series.

Stack trace for ./xmlvalid (from bftools):
*****************************************************************************************************************************************************

ls29010:bftools bramalingam$ ./xmlvalid /Volumes/ome/apache_repo/17373/Z_Time.tif

Parsing schema path

http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd

Validating /Volumes/ome/apache_repo/17373/Z_Time.tif

cvc-pattern-valid: Value 'ome.bitplane.com:ChannelInfo:{82ae6204-0013-4563-9990-949cf96235ee}' is not facet-valid with respect to pattern '(urn:lsid:)?(\S+\.\S+)+(:LogicalChannel)(:\S+)' for type 'LogicalChannelID'.

cvc-attribute.3: The value 'ome.bitplane.com:ChannelInfo:{82ae6204-0013-4563-9990-949cf96235ee}' of attribute 'ID' on element 'ChannelInfo' is not valid with respect to its type, 'LogicalChannelID'.

cvc-complex-type.3.2.2: Attribute 'Description' is not allowed to appear in element 'ChannelInfo'.

cvc-datatype-valid.1.2.1: '600 nm' is not a valid value for 'integer'.

cvc-attribute.3: The value '600 nm' of attribute 'EmWave' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.

cvc-datatype-valid.1.2.1: 'unknown nm' is not a valid value for 'integer'.

cvc-attribute.3: The value 'unknown nm' of attribute 'ExWave' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.

cvc-minInclusive-valid: Value '0' is not facet-valid with respect to minInclusive '1' for type 'positiveInteger'.

cvc-attribute.3: The value '0' of attribute 'PinholeSize' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.

Error validating document: 9 errors found

*************************************************************************************************************************************************************

Hope that helps.

Best,

Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

School of Life Sciences

University of Dundee

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Wednesday, 12 October 2016 at 16:36
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] FW: OMERO.qa - new feedback for QA Bug

Hi James,

Did you open the file using File > Import > Bio-Formats? If you used File > Open, and you don't have the SCIFIO option enabled (in Edit > Options > ImageJ2), then Bio-Formats will not be used, and the fact that the file is an OME-TIFF will not be detected.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Wed, Oct 12, 2016 at 5:21 AM, WAINWRIGHT James <J.Wainwright at andor.com<mailto:J.Wainwright at andor.com>> wrote:
Hi there!

I seem to have problems opening OME TIFF with Bio-Formats, but I can't tell if it's the file or Bio-Formats at fault.

I've uploaded an example dataset as per the below. It has 4 Z and 3 time, but appears in FIJI as 12 time points.

Let me know if I can provide any more information.

Thanks!

James

James Wainwright
Global Applications Specialist - Microscopy Systems

Tel:        +44 (0) 2890 237 126 ext. 2130<tel:%2B44%20%280%29%202890%20237%20126%20ext.%202130>
Skype:  andor.j.wainwright
Mob:     +44 (0) 7834 710 834<tel:%2B44%20%280%29%207834%20710%20834>
Web:     https://www.andor.com/microscopy-systems

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From:qa at openmicroscopy.org.uk<mailto:qa at openmicroscopy.org.uk> [mailto:qa at openmicroscopy.org.uk<mailto:qa at openmicroscopy.org.uk>]
Sent: 12 October 2016 11:09
To: WAINWRIGHT James <J.Wainwright at andor.com<mailto:J.Wainwright at andor.com>>
Subject: OMERO.qa - new feedback for QA Bug

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