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Hi Lionel
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<div class="">I’m not sure if this is of use but the command line tools can be downloaded from <a href="http://downloads.openmicroscopy.org/bio-formats/5.4.0/" class="">http://downloads.openmicroscopy.org/bio-formats/5.4.0/</a></div>
<div class="">“tiffcomment’ can then be used to extract the .xml from a file </div>
<div class="">piping the output to “xmlindent” can be useful for easier reading.</div>
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<div class="">Hope that helps.</div>
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<div class="">Ian</div>
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<div class="">On 3 Apr 2017, at 14:25, Lionel Fafchamps <<a href="mailto:lionel@fafchamps.com" class="">lionel@fafchamps.com</a>> wrote:</div>
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Dear all,
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<div class="">I’ve been using ome-files for some time now as an acquisition format for our in-house microscopy software. When acquiring multichannel data, this works fine until we acquire XY and T data at the same time, as the order of the incoming data would
mean having to close and then reopen an image series with the same writer. I understand that this is expected behaviour, and has been mentioned before on the forums here: </div>
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<div class=""><a href="https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=5812" class="">https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=5812</a></div>
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<div class="">My current strategy is now to split the data into a separate multichannel stack for each xy position and time point. Each one of these files is entirely self-contained with regards to the metadata, so that they can be portable. In addition to
these, I would like to write a companion xml file to bring together everything as a dataset. I’m attempting to do this by setting the companion file tiffdata tags manually to the correct filename/ifd, though as yet it does not seem to work if the UUID of
the file is not also included in the tag.</div>
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<div class="">I’ve tried using the OMETIFFReader to get the uuid/xml comment out of the individual stacks but I haven’t been able to find any function that would let me do so. Does anybody have any suggestions? Additionally, would you consider this a reasonable
way to solve this problem? If there is a better way, I’d be happy to hear of it!</div>
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<div class="">Thanks for your help,</div>
<div class="">Lionel Fafchamps</div>
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