[ome-devel] Reading xml comment with ome-files c++

[Munro, Ian]

Hi Lionel

I’m not sure if this is of use but the command line tools can be downloaded from http://downloads.openmicroscopy.org/bio-formats/5.4.0/
“tiffcomment’ can then be used to extract the .xml from a file
piping the output to “xmlindent” can be useful for easier reading.

Hope that helps.

Ian


On 3 Apr 2017, at 14:25, Lionel Fafchamps <lionel at fafchamps.com<mailto:lionel at fafchamps.com>> wrote:

Dear all,

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:

https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=5812

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.

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!

Thanks for your help,
Lionel Fafchamps
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