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Dear Konrad,
<div class=""><br class="">
</div>
<div class="">following up on this thread, I happened to meet Roberto Spada last week. We went</div>
<div class="">together through an example of the workflow in order to export a multi-page OME-TIFF file</div>
<div class="">using the MCD Viewer. We were able to reproduce the behavior described by Jean-Marie</div>
<div class="">using ImageJ i.e. individual TIFF planes read correctly but the representation of the dataset </div>
<div class="">is incorrect as it fails to be detected as multi-channel.</div>
<div class=""><br class="">
</div>
<div class="">From experience, the primary cause for similar behavior are invalid OME-TIFF files i.e. files</div>
<div class="">that are not compliant with the specification [1]. From the sample dataset shared by Konrad,</div>
<div class="">this is definitely the case as the file suffixed as `.ome.tiff` contains no OME metadata</div>
<div class="">in the ImageDescription tag of the first TIFF IFD. Bio-Formats simply falls back to reading</div>
<div class="">such files as regular multi-page TIFF files. </div>
<div class=""><br class="">
</div>
<div class="">It looks like the way to fix this now lies within the proprietary software. As discussed with</div>
<div class="">Roberto, if technical people at Fluidigm want to get in touch with OME in order to resolve</div>
<div class="">this export issue, they should feel free to continue the discussion here or use any other public</div>
<div class="">support channel [2].</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html" class="">https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html</a> </div>
<div class="">[2] <font color="#0069d9" class=""><span style="caret-color: rgb(0, 105, 217);" class=""><u class=""><a href="https://www.openmicroscopy.org/support/" class="">https://www.openmicroscopy.org/support/</a></u></span></font></div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 7 Nov 2018, at 10:50, Jean-Marie Burel (Staff) <<a href="mailto:j.burel@dundee.ac.uk" class="">j.burel@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi Konrad<br class="">
<br class="">
I tried the data into OMERO. The only one I can import is the OME-TIFF. I<br class="">
have attached the screenshot Is it what you mean by ³blackboxes².<br class="">
There is only one channel and not 7 as indicated in the summary.txt file.<br class="">
<br class="">
I will check the MCD viewer when I have access to a window machine<br class="">
<br class="">
Cheers<br class="">
<br class="">
Jmarie<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 06/11/2018, 10:21, "ome-users on behalf of Kölble, Konrad"<br class="">
<<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of<br class="">
<a href="mailto:Konrad.Koelble@uk-erlangen.de" class="">Konrad.Koelble@uk-erlangen.de</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Hi,<br class="">
the above remains unsolved; Sebastien Burel currently uses a "very<br class="">
non-user friendly way [his words] to create OME metadata files combining<br class="">
the planes from various TIFF files" and suggested to try Fluidigm's MCD<br class="">
Viewer for export. Unfortunately its File-> Open followed by File->Export<br class="">
`.ome.tiff` functionality creates output which blockboxes after OMERO<br class="">
upload.<br class="">
A sample 5-channel down-mix 20170713_spleen50_1_KK-select (together with<br class="">
its parent 2017071313_spleen50_1.txt and an MCD Viewer 1.0 zip-archive)<br class="">
can be found under<br class="">
<br class="">
<a href="https://volafile.org/r/q6aqxn48" class="">https://volafile.org/r/q6aqxn48</a><br class="">
<br class="">
Any brainwaves?<br class="">
<br class="">
Cheers<br class="">
Konrad<br class="">
________________________________________<br class="">
Von: ome-users [ome-users-bounces@lists.openmicroscopy.org.uk]" im<br class="">
Auftrag von "Kölble, Konrad [Konrad.Koelble@uk-erlangen.de]<br class="">
Gesendet: Mittwoch, 31. Oktober 2018 14:51<br class="">
An: ome-users@lists.openmicroscopy.org.uk<br class="">
Betreff: [ome-users] 12-channel Imaging Mass Cytometry -> OMERO<br class="">
<br class="">
Hi,<br class="">
recently Fluidigm's Roberto Spada sent me a 12-marker human spleen FFPE<br class="">
1mm2 section's Hyperion Imaging System dataset at the standard 1um2<br class="">
resolution including<br class="">
<br class="">
- an original raw 2017071313_spleen50_1.txt file<br class="">
- MCD Viewer software which opens such *.txt files for analysis and<br class="">
generation of original .ome.tiff or false color TIFF files<br class="">
- original raw 16-bit and/or 32-bit .ome.tiff images<br class="">
<br class="">
Has someone successfully managed to OMEROze pic & metadata output from<br class="">
this interesting instrument<br class="">
https://www.fluidigm.com/products/hyperion-imaging-system<br class="">
for multichannel viewing?<br class="">
<br class="">
You'll find the 2017071313_spleen50_1.txt, the MCD Viewer (incl. guide),<br class="">
the 16bit tiff and the 32bit tiff images under<br class="">
https://volafile.org/r/q1h07r5m<br class="">
<br class="">
Cheers<br class="">
Konrad<br class="">
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</blockquote>
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<br class="">
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