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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">Dear everyone,</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">following recent threads posted both on the OME mailing list [1] and on the Micro-Manager</span></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">mailing list [2], we have updated Bio-Formats to support parsing of Micro-Manager
metadata stored in JSON format [3].</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">For users wanting to benefit from these improvements:</span></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">- if the data is saved as “Separate Image Files”, the metadata should be automatically
read</span></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">- if the data is saved as “Image Stack Files”, then the “Create metadata.txt
file with Image Stack Files” needs to be selected in the Tools > options menu. Clients using Bio-Formats (ImageJ/Fiji, OMERO, Icy…) should point at the metadata.txt file and not the .ome.tif. file(s) in order to parse the JSON metadata [4]</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">These additions have been released as part of Bio-Formats 5.1.8 and will be bundled
with the next release of OMERO. Note that for data saved image file stack to load properly, both the OMERO server and the client used for importing data will need to be upgraded to 5.2.2.</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">Many thanks to Thomas Julou and Chris Weisiger for their input and the shared
datasets [5].</span></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">Supporting custom metadata formats is important, but also challenging for us
and the wider community. A larger discussion about the utility of OME’s metadata tools, OME's response to continuing requests for updates and changes, and the best extension points for Micro-Manager and others, is clearly necessary. Note that our next proposal
for Bio-Formats support and development aims to improve these extension points [6]. More Letters of Support are welcome!!!</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">Best,</span></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">The OME team</span></div>
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<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[1] </span><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005825.html" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005825.html</span></a></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[2] </span><a href="http://micro-manager.3463995.n2.nabble.com/Loading-MM2-datasets-with-bioformats-scifio-td7586511.html#a7586596" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">http://micro-manager.3463995.n2.nabble.com/Loading-MM2-datasets-with-bioformats-scifio-td7586511.html#a7586596</span></a></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[3] </span><a href="https://micro-manager.org/wiki/Micro-Manager_File_Formats" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">https://micro-manager.org/wiki/Micro-Manager_File_Formats</span></a></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[4] </span><a href="https://www.openmicroscopy.org/site/support/bio-formats5.1/formats/micro-manager.html" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">https://www.openmicroscopy.org/site/support/bio-formats5.1/formats/micro-manager.html</span></a></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[5] </span><a href="http://downloads.openmicroscopy.org/images/Micro-Manager" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">http://downloads.openmicroscopy.org/images/Micro-Manager</span></a></div>
<div class="" style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; vertical-align: baseline;">[6] </span><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-February/005853.html" class="" style="text-decoration: none;"><span class="" style="font-size: 14.666666666666666px; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline;">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-February/005853.html</span></a></div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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