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Dear Susanne,
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<div class="">You are right, the fix for this particular issue was carried out at the Bio-Formats level specifically</div>
<div class="">as part of this Pull Request [1] and was released together with Bio-Formats 5.2.0.</div>
<div class=""><br class="">
</div>
<div class="">The fix unfortunately did not get backported to the 5.1.x line. However, looking at the diff it does</div>
<div class="">not seem to require any 5.2.0 specific feature. So it should be possible to integrate it into a local</div>
<div class="">development version of Bio-Formats.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/pull/2221" class="">https://github.com/openmicroscopy/bioformats/pull/2221</a></div>
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<blockquote type="cite" class="">
<div class="">On 14 Sep 2016, at 12:44, Kunis, Susanne <<a href="mailto:Susanne.Kunis@Biologie.Uni-Osnabrueck.DE" class="">Susanne.Kunis@Biologie.Uni-Osnabrueck.DE</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Mark,<br class="">
<br class="">
thank you for your explanations, but the command-line access is not a solution for the users of our facility.<br class="">
<br class="">
This is what i've try:<br class="">
(I used ImageJ 1.50b)<br class="">
# + Plugin Bio-Formats 5.1.8 load image file from local disc - works<br class="">
# +Plugin Bio-Formats 5.1.8 Import from local disc - failed<br class="">
<br class="">
# +Plugin Bio-Formats 5.2.2 load image from local disc - works<br class="">
# +Plugin Bio-Formats 5.2.2 Remote Importer throws an exception:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"></span>java.lang.NegativeArraySizeException<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:559)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.OMEXMLReader.isThisType(OMEXMLReader.java:100)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.isThisType(FormatReader.java:619)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.OMEXMLReader.isThisType(OMEXMLReader.java:111)<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ImageReader.getReader(ImageReader.java:181)<br class="">
<br class="">
# +Plugin Bio-Formats 5.2.2 Import from local disc - works<br class="">
<br class="">
The Remote Importer of Bio-Formats doesn't seem to access only the raw image on server? Or what ist the reason of this behaviour?<br class="">
<br class="">
Do it understand it right, it is a problem of Bio-Formats? Maybe it could be a solution that i integrate the fixed code in my local Bio-Formats 5.1.8 , if the fix isn't so much invasiv...<br class="">
I already looked for it at the GIT, but maybe you have a hint for me?<br class="">
<br class="">
Cheers<br class="">
Susanne<br class="">
<br class="">
-----Ursprüngliche Nachricht-----<br class="">
Von: ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>] Im Auftrag von Mark Carroll<br class="">
Gesendet: Dienstag, 13. September 2016 14:25<br class="">
An: <a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
Betreff: Re: [ome-users] Viewer shows Zeiss SEM Auriga data as blank [5.2.4]<br class="">
<br class="">
On 09/13/2016 01:16 PM, Mark Carroll wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Easier and more likely to work is to use the Bio-Formats 5.2.2
<br class="">
command-line tools with the original file separately from OMERO.<br class="">
</blockquote>
<br class="">
Of course, I should have added that the 5.2.2 version of bioformats_package.jar also works just fine in ImageJ, I didn't mean to single out the command-line tools in particular so much as to say "separately from OMERO 5.2". You might still need to import the
file into ImageJ from your local disk but /perhaps/ you could just use the plugin's "Bio-Formats Remote Importer" with your current server and see if it works directly too.<br class="">
<br class="">
-- Mark<br class="">
<br class="">
The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________<br class="">
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</blockquote>
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<br class="">
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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