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<div class="">On 21 Feb 2017, at 16:09, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" class="">qigong@gwmail.gwu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello everyone,</div>
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<div>Hi Qi</div>
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<div class="">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 class="">Let me make sure we get your workflow right:<br class="">
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<div class="">- WSI images and their ROIs are read inside a MATLAB software using Bio-Formats<br class="">
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<div class="">- this MATLAB code also annotates the ROI and saves the output as an XML file<br class="">
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<div class="">- You would like both the WSI image and the annotated ROI to be opened jointly by</div>
<div class=""> 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 class="">annotation publicly available?</span></div>
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<div class="">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 class="">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 class="">
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<div><span class="">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 class="">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" class="">https://trac.openmicroscopy.org/ome/ticket/10504</a><br class="">
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<div class="">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 class="">
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<div class="">Regards,</div>
<div class="">Qi<br clear="all" class="">
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Best,</div>
<div>Sebastien<br class="">
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