[ome-users] Question about XML annotation file.

[Sebastien Besson (Staff)]

On 21 Feb 2017, at 16:09, Qi Gong <qigong at gwmail.gwu.edu<mailto:qigong at gwmail.gwu.edu>> wrote:

Hello everyone,

Hi Qi

We are using Bio-format to extract ROI from WSI image in Matlab. At the same time, we also want to open manufacturer viewer (imagescope) to open the WSI image with an annotation of the ROI. We have used matlab to generate the XML annotation file. But every time we have to manually use imagescope viewer GUI to load the XML file.

Let me make sure we get your workflow right:

- WSI images and their ROIs are read inside a MATLAB software using Bio-Formats
- this MATLAB code also annotates the ROI and saves the output as an XML file
- You would like both the WSI image and the annotated ROI to be opened jointly by
  the Imagescope software

Is that a correct representation of your workflow? Out of curiosity, is the code doing the
annotation publicly available?

We want to know, does Bioformat provides a function to use command line to apply XML file on WSI image.

I assume that applying the XML file on WSI image means formatting your XML file in such a way that it can be detected by ImageScope.

Within OME, we certainly have an existing ticket for reading these XML files in Bio-Formats [1]. I think this issue is symmetrical to
to the enquiry you have about writing these files. One of our current limitations is that we do not have a proper specification for these
annotation XML files. Do you happen to know if such a thing exists?

For your use case, a secondary issue is to know how Imagescope detects an XML file associated with an WSI image. A simple
assumption would be that this is based on some naming conventions but this would have to be checked with the constructor or
confirmed by the community.

[1] https://trac.openmicroscopy.org/ome/ticket/10504


Is "xmlindent" a potential function? Thank you.

I would not think this utility function will be of any help for this problem as its main purpose is to indent an existing XML.


Regards,
Qi

Best,
Sebastien

--
mobile phone: 2024060862
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170222/de964a97/attachment.html>