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Dear Mai,
<div class=""><br class="">
</div>
<div class="">the fix for your LIF issue has been reviewed by the OME team and merged three days</div>
<div class="">ago into the development line (for reference the changes were finally handled in</div>
<div class=""><a href="https://github.com/openmicroscopy/bioformats/pull/1724" class="">https://github.com/openmicroscopy/bioformats/pull/1724</a>).</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">This bug fix will be included in the next 5.1.1 release of Bio-Formats due by the end of this</div>
<div class="">month.</div>
</div>
<div class=""><br class="">
</div>
<div class="">As you are using Fiji, the easiest way to retrieve the latest version of Bio-Formats including</div>
<div class="">this bug fix immediately is to enable the Bio-Formats update site following the instructions given</div>
<div class="">by Mark below (<a href="http://imagej.net/How_to_follow_a_3rd_party_update_site" class="">http://imagej.net/How_to_follow_a_3rd_party_update_site</a>).</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div>
<blockquote type="cite" class="">
<div class="">On 14 Apr 2015, at 13:11, Mark Hiner <<a href="mailto:hiner@wisc.edu" class="">hiner@wisc.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">Hi all,<br class="">
<br class="">
>Can you briefly tell me what I need to do exactly in Fiji to be able to read my file with the solution.<br class="">
<br class="">
>For Fiji, it's a bit more annoying because you first have to remove all the existing files related to bioformats before doing this.
<br class="">
<br class="">
</div>
Note that Roger's instructions only apply to testing Fiji/ImageJ with unmerged branches. Once
<a href="https://github.com/openmicroscopy/bioformats/pull/1724" class="">https://github.com/openmicroscopy/bioformats/pull/1724</a> is merged, all you need to do is enable the Bio-Formats update site (<a href="http://imagej.net/How_to_follow_a_3rd_party_update_site" class="">http://imagej.net/How_to_follow_a_3rd_party_update_site</a>)
which is synchronized with the develop branch (<a href="https://github.com/openmicroscopy/bioformats" class="">https://github.com/openmicroscopy/bioformats</a>). You would not need to manually modify any .jars, and should not need to wait for a 5.1.1 release
to test this fix.<br class="">
<br class="">
</div>
But note that even with this patch on the Bio-Formats update site, using a non-release version of Bio-Formats gives up reproducibility (<a href="http://imagej.net/Architecture#Reproducible_builds" class="">http://imagej.net/Architecture#Reproducible_builds</a>)
and should only be used for testing - as Roger suggested.<br class="">
<br class="">
</div>
Best,<br class="">
</div>
Mark<br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, Apr 14, 2015 at 3:57 AM, Roger Leigh <span dir="ltr" class="">
<<a href="mailto:rleigh@dundee.ac.uk" target="_blank" class="">rleigh@dundee.ac.uk</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span class="">On 13/04/15 19:54, Mai Tran wrote:<br class="">
</span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Roger,<br class="">
<br class="">
<span class="">I'm new to using Fiji and coding. Can you briefly tell me what I need to<br class="">
do exactly in Fiji to be able to read my file with the solution. My<br class="">
guess is I need to append the provided code into my current Bioformat<br class="">
plugins but I don't know how to access the Bioformat code in window8.<br class="">
</span></blockquote>
<br class="">
You can obtain the current build with this change merged in here:<br class="">
<br class="">
<br class="">
<a href="https://ci.openmicroscopy.org/job/BIOFORMATS-5.1-merge-build/lastSuccessfulBuild/artifact/artifacts/" target="_blank" class="">https://ci.openmicroscopy.org/<u class=""></u>job/BIOFORMATS-5.1-merge-<u class=""></u>build/lastSuccessfulBuild/<u class=""></u>artifact/artifacts/</a><br class="">
<br class="">
For plain ImageJ, you can use either loci_tools.jar or<br class="">
bioformats_package.jar; just download and copy to the plugins directory<br class="">
and restart ImageJ.<br class="">
(<a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/#upgrading" target="_blank" class="">http://www.openmicroscopy.<u class=""></u>org/site/support/bio-formats5.<u class=""></u>1/users/imagej/#upgrading</a>)<br class="">
<br class="">
For Fiji, it's a bit more annoying because you first have to remove all<br class="">
the existing files related to bioformats before doing this. See<br class="">
<br class="">
<br class="">
<a href="https://github.com/bramalingam/bioformats/blob/Doc_Fiji_BFUpdate/docs/sphinx/users/fiji/index.txt" target="_blank" class="">https://github.com/<u class=""></u>bramalingam/bioformats/blob/<u class=""></u>Doc_Fiji_BFUpdate/docs/sphinx/<u class=""></u>users/fiji/index.txt</a><br class="">
<br class="">
for some proposed instructions for doing this (it assumes the version is<br class="">
5.0.7; just replace this with the version Fiji is currently using).<br class="">
<br class="">
You might find it easier, for testing purposes, to use plain ImageJ<br class="">
though. When 5.1.1 is released, it should be updated in Fiji shortly after.
<div class="HOEnZb">
<div class="h5"><br class="">
<br class="">
<br class="">
Kind regards,<br class="">
Roger<br class="">
<br class="">
--<br class="">
Dr Roger Leigh -- Open Microscopy Environment<br class="">
Wellcome Trust Centre for Gene Regulation and Expression,<br class="">
College of Life Sciences, University of Dundee, Dow Street,<br class="">
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br class="">
<br class="">
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
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</div>
</blockquote>
</div>
<br class="">
</div>
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</blockquote>
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