[ome-users] Import plate data from the FEI MORE as screen in OMERO

[Sebastien Besson (Staff)]

Hi Kai,

sorry for the delay. We have been looking at some ways to prototype the generation of
companion OME files lately. You might want to take a look at [1] [2] which are using
xml.etree to construct synthetic examples. As indicated, this is definitely ongoing
experimental work so feedback very welcome.

Best,
Sebastien

[1] https://github.com/ome/ome-model/pull/91
[2] https://github.com/ome/ome-model/pull/92


> On 16 Nov 2018, at 14:55, Kai Schleicher <kai.schleicher at unibas.ch> wrote:
>
> Hi Mark,
>
> thank you very much once again for your helpful mail!
>
> I really appreciate your time supporting my vague questions :)
>
> Now that I have reached an understanding of what needs to be done and also how to do it, I think the path is set.
>
>> I'm afraid you do have a bit of programming ahead of you: what you need
>> is certainly possible but also not trivial.
>
> I am getting more and more familiar with python (for scripting imageJ anyway), so I started looking into suitable modules and found xml.dom.minidom, but I am new in manipulating XML files.
>
>> If you'd like a Python example of how to generate something like the
>> companion file you'd need then we could try to construct one for you.
> that would be amazing!! Thank you so much!
>
> I will try and see what I can do on my own of course, but needless to say an example by you would be brilliant!
>
> Thank you again and cheers,
> Kai
>
> On 11/16/18 12:42 PM, Mark Carroll (Staff) wrote:
>> Dear Kai,
>>
>> Yes, I think you need to write your own companion file (very similar to
>> what you already have among the OME-TIFFs) and put the simple XML in the
>> OME-TIFFs that, via filename and UUID as I had in my example, describes
>> the relationship among the companion and its TIFFs.
>>
>> I'm afraid we don't have easy code handy that would be a helpful basis
>> for doing this work. Fortunately your XML is already fairly close to
>> what it should be and the mainstream programming languages these days
>> have decent DOM manipulation libraries so my suggestion would be to
>> avoid regular expressions and instead use some XML library to read, fix
>> and write. tiffcomment can read and write the XML from the TIFFs. But,
>> you would have to get to grips with coding using some XML library to
>> make the required adjustments.
>>
>> An alternative approach might be to use the example of our XML service
>> code such as the Java implementation in
>> https://github.com/ome/ome-common-java/tree/master/src/main/java/loci/common
>> to figure out how to read the XML into a OMEXMLMetadataImpl, manipulate
>> it via that class' API, then write it out again. However, the source in
>> that module is probably about all the documentation you're getting on
>> how to do that and there are some gotchas, so I think you'd have an
>> easier time avoiding that route and just working with the XML DOM instead.
>>
>> If you'd like a Python example of how to generate something like the
>> companion file you'd need then we could try to construct one for you.
>> I'm afraid you do have a bit of programming ahead of you: what you need
>> is certainly possible but also not trivial.
>>
>> You might be interested to know that in due course we hope to relax the
>> companion file requirements so that you could have a single OME-XML
>> document for your plate that references a set of simple TIFFs instead of
>> requiring OME-XML headers also in those TIFFs.
>>
>> -- Mark
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
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