<div dir="ltr">Hi Roger,<div><br></div><div><div>> I've done some further testing with the submitted files.</div></div><div><br></div><div>Thank you very much for the further testing.</div><div><br></div><div><div>> Workarounds for broken data should never compromise the handling of</div><div>> valid data, and at some point there is a limit for what it is</div><div>> reasonable or safe for us to correct.</div></div><div><br></div><div>I absolutely agree 100%. However, two points in this case:</div><div><br></div><div>1) I believe these files were written by Bio-Formats itself. I would argue that under no circumstances should Bio-Formats write OME-TIFFs which are later considered to be invalid or corrupt. Even dev builds of Bio-Formats should use a stable schema version by default. If it is needed for testing to write files with "in-progress" schemas, that option should be specified via a manually triggered API call, rather than happen by default.</div><div><br></div><div><div>2) For files with an "in-progress" schema version, making a best effort to parse using nearby stable schema versions does not introduce any possibility of compromise to valid data handling. So I am glad to hear that Bio-Formats does this.</div><div><br></div></div><div><div>> I'd be interested to know why it wasn't working for you with your</div><div>> Fiji/ImageJ installation.</div></div><div><br></div><div>Michael: can you describe the exact steps you took? Grid/Collection Stitching? Which parameters? Which version of Fiji + Java are you using? Click the status bar to see.</div><div><br></div><div>Regards,<br></div><div>Curtis</div><div class="gmail_extra"><br clear="all"><div><div class="gmail-m_-3553053888379761269m_8669640508856335025gmail-m_-4769113813906993667m_3286085737791209170gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="http://loci.wisc.edu/software" target="_blank">http://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="http://imagej.net/User:Rueden" target="_blank">http://imagej.net/User:Ruede<wbr>n</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Nov 10, 2016 at 7:32 AM, Roger Leigh <span dir="ltr"><<a href="mailto:rleigh@dundee.ac.uk" target="_blank">rleigh@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear all,<br>
<br>
I've done some further testing with the submitted files. They are<br>
technically invalid (non-validating), but I can in practice I can:<br>
<br>
- view them with showinf,<br>
- convert them to 2016-06 OME-TIFF with bfconvert (fixing the validation<br>
errors)<br>
- import into current Fiji (with the java8 update site providing<br>
bioformats 5.2.4)<br>
<br>
None of these showed any errors for me.<br>
<br>
So it looks like Bio-Formats is already doing the "best effort"<br>
transformation in this particular case. I'd be interested to know why<br>
it wasn't working for you with your Fiji/ImageJ installation. Were you<br>
using the current version of Bio-Formats (5.2.4) with the Java8 update site?<br>
<br>
I would highly recommend running bfconvert on these files to transform<br>
them into valid OME-TIFF data.<br>
<br>
A final comment about this type of "best effort" handling of invalid<br>
data. Bio-Formats already makes significant efforts to cope with<br>
various different types of invalid data and metadata so that broken,<br>
damaged and incorrect files can be read. However, this does come at a<br>
cost. As an example, a few weeks ago a fix to handle broken TiffData<br>
elements in OME-TIFF was found to corrupt *valid* OME-TIFF data due to<br>
certain assumptions being made about the structure of the data. That<br>
is, it altered the original (and correct) intent of the data.<br>
Workarounds for broken data should never compromise the handling of<br>
valid data, and at some point there is a limit for what it is reasonable<br>
or safe for us to correct. Broken data must at some point result in a<br>
hard failure. Not notifying the user that the data is incorrect is<br>
helpful from one point of view (getting the data read so we can get work<br>
done), but longer term it masks serious problems from both users and<br>
developers and delays getting them fixed. And it can also result in<br>
software using Bio-Formats unknowingly creating buggy OME-TIFFs; the<br>
workarounds result in problems not being picked up during testing<br>
because it appears to "work" while actually being broken. This is bad<br>
for interoperability, and also for the complexity of the OME-TIFF<br>
reader, which then needs to permanently retain a whole series of<br>
workarounds for every buggy file in existence rather than simply<br>
implementing the standard, and that burden is already unreasonably high.<br>
In this particular case, the workaround is (by chance) safe and<br>
functional, but development versions of the schema should never have<br>
been used for writing OME-TIFF; only published finalised versions of the<br>
schema are suitable for use in the OME-TIFF file format, and trying to<br>
use development versions for long term archival is asking for<br>
trouble--we make no guarantees these can be read back in since<br>
incompatible changes to the schema before release would result in<br>
untransformable data. The transforms are only provided for and tested<br>
with published released versions of the schema.<br>
<br>
<br>
Regards,<br>
Roger<span><br>
<br>
On 09/11/16 20:17, Curtis Rueden wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span>
Hi,<br>
<br>
Michael: This problem would occur if WiscScan was ever deployed to use a<br>
non-release version of Bio-Formats. Ask the WiscScan programmers to<br>
search the Git commit history for changes to the Bio-Formats JAR files,<br>
to see which versions were committed when.<br>
<br>
OME team: it would be nice if Bio-Formats could make a "best effort" to<br>
transform these sorts of files, by attempting to treat them as one or<br>
more released schema versions before giving up on the XSLT forward<br>
transform.<br>
<br>
Regards,<br>
Curtis<br>
<br>
--<br>
Curtis Rueden<br>
LOCI software architect - <a href="http://loci.wisc.edu/software" rel="noreferrer" target="_blank">http://loci.wisc.edu/software</a><br>
ImageJ2 lead, Fiji maintainer - <a href="http://imagej.net/User:Rueden" rel="noreferrer" target="_blank">http://imagej.net/User:Rueden</a><br>
<<a href="http://imagej.net/User:Rueden" rel="noreferrer" target="_blank">http://imagej.net/User:Rueden</a><wbr>><br>
Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" rel="noreferrer" target="_blank">http://forum.imagej.net/</a><br>
<br>
<br>
On Wed, Nov 9, 2016 at 2:03 PM, Michael Pinkert <<a href="mailto:mpinkert@wisc.edu" target="_blank">mpinkert@wisc.edu</a><br></span><span>
<mailto:<a href="mailto:mpinkert@wisc.edu" target="_blank">mpinkert@wisc.edu</a>>> wrote:<br>
<br>
Thanks for solving that Roger!<br>
<br>
That solution makes sense, though it is rather confusing that we<br>
would be encountering this problem now. We've been using the<br>
software for years without problems, but I guess an update either<br>
messed up the references or made the improper reference a<br>
requirement when it wasn't before.<br>
<br>
I'll have to talk to the more knowledgeable coders on this issue,<br>
and look around to see if other people are still having this problem.<br>
<br>
Best regards,<br>
Michael Pinkert<br>
<br>
-----Original Message-----<br>
From: ome-users<br>
[mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@list<wbr>s.openmicroscopy.org.uk</a><br>
<mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@list<wbr>s.openmicroscopy.org.uk</a>>] On Behalf Of<br>
Roger Leigh<br>
Sent: Wednesday, November 9, 2016 4:20 AM<br>
To: <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br></span><div><div class="gmail-m_-3553053888379761269m_8669640508856335025gmail-m_-4769113813906993667m_3286085737791209170h5">
<mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmi<wbr>croscopy.org.uk</a>><br>
Subject: Re: [ome-users] Bug report for version 2012-06 OME-XML in<br>
Fiji, seen in grid/collection stitching<br>
<br>
On 08/11/16 19:50, Michael Pinkert wrote:<br>
> Hi Mark,<br>
><br>
> I just uploaded 9 files, from a much smaller sample image set. I<br>
tried using the ImageJ/Fiji stitching algorithm again with this<br>
smaller sample size and it ran into the same problem, with the same<br>
warning. It seems not to be reading the metadata correctly, because<br>
it was interpreting different Z-slices as different T-time points.<br>
><br>
> This problem occurred after a recent Fiji/ImageJ update and<br>
applies to older sets of images that I've already stitched; I don't<br>
think there's anything wrong with the formatting of the images.<br>
<br>
Dear Michael,<br>
<br>
I've taken a look at your files, and the problem is that the XML<br>
schema is invalid. Using bftools' xmlvalid program:<br>
<br>
% ./tools/xmlvalid ~/images/17416/FijiTester.ome.<wbr>xml Parsing schema<br>
path<br>
<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmic<wbr>roscopy/openmicroscopy/schema-<wbr>2012-06/components/specificati<wbr>on/InProgress/ome.xsd</a><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>><br>
Validating /home/rleigh/images/17416/Fiji<wbr>Tester.ome.xml<br>
Error parsing schema at<br>
<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmic<wbr>roscopy/openmicroscopy/schema-<wbr>2012-06/components/specificati<wbr>on/InProgress/ome.xsd</a><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>><br>
org.xml.sax.SAXParseException: schema_reference.4: Failed to read<br>
schema document<br>
'<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>>',<br>
because 1) could not find the document; 2) the document could not be<br>
read; 3) the root element of the document is not <xsd:schema>.<br>
<br>
% ./tools/xmlvalid ~/images/17416/FijiTester_C0_T<wbr>P0_SP0_FW0.ome.tiff<br>
Parsing schema path<br>
<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmic<wbr>roscopy/openmicroscopy/schema-<wbr>2012-06/components/specificati<wbr>on/InProgress/ome.xsd</a><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>><br>
Validating /home/rleigh/images/17416/Fiji<wbr>Tester_C0_TP0_SP0_FW0.ome.tiff<br>
Error parsing schema at<br>
<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmic<wbr>roscopy/openmicroscopy/schema-<wbr>2012-06/components/specificati<wbr>on/InProgress/ome.xsd</a><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>><br>
org.xml.sax.SAXParseException: schema_reference.4: Failed to read<br>
schema document<br>
'<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a><br></div></div><span>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>>',<br>
because 1) could not find the document; 2) the document could not be<br>
read; 3) the root element of the document is not <xsd:schema>.<br>
<br>
<br>
The schema which is being used here is an invalid URL, and was never<br>
a released schema. I'm not sure why any software would be using that.<br>
<br>
You can find sample files using the old 2012-06 schema here:<br>
<a href="http://downloads.openmicroscopy.org/images/OME-TIFF/2012-06/" rel="noreferrer" target="_blank">http://downloads.openmicroscop<wbr>y.org/images/OME-TIFF/2012-06/</a><br>
<<a href="http://downloads.openmicroscopy.org/images/OME-TIFF/2012-06/" rel="noreferrer" target="_blank">http://downloads.openmicrosco<wbr>py.org/images/OME-TIFF/2012-06<wbr>/</a>><br>
They are using a root element like this:<br>
<br>
<OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicrosco<wbr>py.org/Schemas/OME/2012-06</a><br>
<<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/OME/2012-06</a>>"<br>
xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" rel="noreferrer" target="_blank">http://www.w3.org/2<wbr>001/XMLSchema-instance</a><br>
<<a href="http://www.w3.org/2001/XMLSchema-instance" rel="noreferrer" target="_blank">http://www.w3.org/2001/XMLSch<wbr>ema-instance</a>>"<br>
xmlns:ROI="<a href="http://www.openmicroscopy.org/Schemas/ROI/2012-06" rel="noreferrer" target="_blank">http://www.openmicr<wbr>oscopy.org/Schemas/ROI/2012-06</a><br>
<<a href="http://www.openmicroscopy.org/Schemas/ROI/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/ROI/2012-06</a>>"<br>
xmlns:SA="<a href="http://www.openmicroscopy.org/Schemas/SA/2012-06" rel="noreferrer" target="_blank">http://www.openmicro<wbr>scopy.org/Schemas/SA/2012-06</a><br>
<<a href="http://www.openmicroscopy.org/Schemas/SA/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/SA/2012-06</a>>"<br>
xmlns:SPW="<a href="http://www.openmicroscopy.org/Schemas/SPW/2012-06" rel="noreferrer" target="_blank">http://www.openmicr<wbr>oscopy.org/Schemas/SPW/2012-06</a><br>
<<a href="http://www.openmicroscopy.org/Schemas/SPW/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/SPW/2012-06</a>>"<br>
<br>
xmlns:Bin="<a href="http://www.openmicroscopy.org/Schemas/BinaryFile/2012-06" rel="noreferrer" target="_blank">http://www.openmicr<wbr>oscopy.org/Schemas/BinaryFile/<wbr>2012-06</a><br>
<<a href="http://www.openmicroscopy.org/Schemas/BinaryFile/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/BinaryFile/2012-06</a>>"<br>
<br>
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www<wbr>.openmicroscopy.org/Schemas/OM<wbr>E/2012-06</a> <<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/OME/2012-06</a>><br></span>
<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd" rel="noreferrer" target="_blank">http://www.openmicroscopy.org/<wbr>Schemas/OME/2012-06/ome.xsd</a><span><br>
<<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06/ome.xsd" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/OME/2012-06/ome.xsd</a>>"<wbr>><br>
<br>
while your samples do this:<br>
<br>
<OME xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicrosco<wbr>py.org/Schemas/OME/2012-06</a><br></span><span>
<<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/OME/2012-06</a>>"<br>
xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" rel="noreferrer" target="_blank">http://www.w3.org/2<wbr>001/XMLSchema-instance</a><br></span>
<<a href="http://www.w3.org/2001/XMLSchema-instance" rel="noreferrer" target="_blank">http://www.w3.org/2001/XMLSch<wbr>ema-instance</a>>"<br>
<br>
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www<wbr>.openmicroscopy.org/Schemas/OM<wbr>E/2012-06</a> <<a href="http://www.openmicroscopy.org/Schemas/OME/2012-06" rel="noreferrer" target="_blank">http://www.openmicroscopy.org<wbr>/Schemas/OME/2012-06</a>><br>
<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmic<wbr>roscopy/openmicroscopy/schema-<wbr>2012-06/components/specificati<wbr>on/InProgress/ome.xsd</a><span><br>
<<a href="https://raw.github.com/openmicroscopy/openmicroscopy/schema-2012-06/components/specification/InProgress/ome.xsd" rel="noreferrer" target="_blank">https://raw.github.com/openmi<wbr>croscopy/openmicroscopy/schema<wbr>-2012-06/components/specificat<wbr>ion/InProgress/ome.xsd</a>>"><br>
<br>
It's the schemaLocation which is wrong, making the file invalid. If<br>
you fix that up, and the rest of the file is valid for the 2012-06<br>
schema, it should then work correctly.<br>
<br>
<br>
Kind regards,<br>
Roger<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre<br>
for Gene Regulation and Expression, College of Life Sciences,<br>
University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No:<br>
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<br>
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</span></blockquote><div class="gmail-m_-3553053888379761269m_8669640508856335025gmail-m_-4769113813906993667m_3286085737791209170HOEnZb"><div class="gmail-m_-3553053888379761269m_8669640508856335025gmail-m_-4769113813906993667m_3286085737791209170h5">
<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</div></div></blockquote></div><br></div></div>