<div dir="ltr">Hello <span style="font-size:12.8px">Sebastien</span>,<div><br></div><div>Thank you for your reply. Yes, the <span style="font-size:12.8px">workflow</span><span style="font-size:12.8px"> is correct. In attachment, I use matlab function "xmlwrite" to generate the xml file. We will also put the function on GITHUB. I find the problem is that, the xml file is generated by xmlwrite always has </span><span style="font-size:12.8px">XML encoding tag "<?xml version="1.0" encoding="UTF-8"?>". It prevents imagescope to load the XML. I have submit a mathwork ticket. Hope I can get a solution. Thank you again.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Regards,</span></div><div><span style="font-size:12.8px">Qi</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 22, 2017 at 3:42 PM, Sebastien Besson (Staff) <span dir="ltr"><<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>On 21 Feb 2017, at 16:09, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" target="_blank">qigong@gwmail.gwu.edu</a>> wrote:</div>
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<div dir="ltr">Hello everyone,</div>
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<div>Hi Qi</div><span class="">
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<div>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.
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</span><span>Let me make sure we get your workflow right:<br>
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<div>- WSI images and their ROIs are read inside a MATLAB software using Bio-Formats<br>
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<div>- this MATLAB code also annotates the ROI and saves the output as an XML file<br>
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<div>- You would like both the WSI image and the annotated ROI to be opened jointly by</div>
<div> the Imagescope software</div>
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Is that a correct representation of your workflow? Out of curiosity, is the code doing the</span></div>
<div><span>annotation publicly available?</span></div>
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<div>We want to know, does Bioformat provides a function to use command line to apply XML file on WSI image.</div>
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</span><span>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.<br>
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<div><span>Within OME, we certainly have an existing ticket for reading these XML files in Bio-Formats [1]. I think this issue is symmetrical to</span></div>
<div>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</div>
<div>annotation XML files. Do you happen to know if such a thing exists?</div>
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For your use case, a secondary issue is to know how Imagescope detects an XML file associated with an WSI image. A simple</span></div>
<div><span>assumption </span>would be that this is based on some naming conventions but this would have to be checked with the constructor or</div>
<div>confirmed by the community.</div>
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[1] <a href="https://trac.openmicroscopy.org/ome/ticket/10504" target="_blank">https://trac.<wbr>openmicroscopy.org/ome/ticket/<wbr>10504</a><br>
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<div>Is "xmlindent" a potential function? Thank you.</div>
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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. <br>
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<div>Regards,</div>
<div>Qi<br clear="all">
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Best,</div>
<div>Sebastien<br>
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