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

[Simone Leo]

Hi Lionel,

In addition to what Ian suggested for reading the XML metadata out of an
OME-TIFF file, since Bio-Formats 5.4.0 you can also write a dataset as
binary-only OME-TIFF + companion XML file. The relevant PR is
https://github.com/openmicroscopy/bioformats/pull/2773, which also
contains some command line examples.

Regards,

Simone

On 03/04/2017 15:49, Munro, Ian wrote:
> 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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>
>
>
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