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<p class="MsoNormal"><span style="color:black">Ali,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Take a look at QuPath and read through the docs.
<a href="https://qupath.github.io/">https://qupath.github.io/</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">It has built in tools to export tiles, included labeled image masks, for deep learning projects:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="https://qupath.readthedocs.io/en/stable/docs/advanced/exporting_annotations.html?highlight=export%20tiles#binary-labeled-images">https://qupath.readthedocs.io/en/stable/docs/advanced/exporting_annotations.html?highlight=export%20tiles#binary-labeled-images</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">You will need to develop a script to convert the NDPI annotations into QuPath annotations. Search around on the active user forums, as someone may have already posted a similar question, e.g.
<a href="https://forum.image.sc/t/importing-ndpa-annotation-files-into-qupath-code-attached/33721">
https://forum.image.sc/t/importing-ndpa-annotation-files-into-qupath-code-attached/33721</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Kind Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Jonathan Henriksen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959">Laboratory Medicine and Pathology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959">Digital Pathology Coordinator for
</span><span style="font-size:9.0pt;color:#595959">Anatomic Pathology</span><span style="font-size:9.0pt;color:#595959"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959">Research IT Coordinator for
</span><span style="font-size:9.0pt;color:#595959">NWBioSpecimen Shared Resource</span><span style="font-size:9.0pt;color:#595959"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959">University of Washington<o:p></o:p></span></p>
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