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<p class="MsoNormal"><a name="_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Mr Gong,<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">You may find the following links interesting.<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Desktop applications:<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">ASAP:
</span></span><a href="https://github.com/GeertLitjens/ASAP"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">https://github.com/GeertLitjens/ASAP</span></span><span style="mso-bookmark:_MailEndCompose"></span></a><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">QuPath:
</span></span><a href="https://qupath.github.io/"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">https://qupath.github.io/</span></span><span style="mso-bookmark:_MailEndCompose"></span></a><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Web-based:<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Cytomine:
</span></span><a href="https://cytomine.coop/"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">https://cytomine.coop/</span></span><span style="mso-bookmark:_MailEndCompose"></span></a><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Pathomation:
</span></span><a href="http://free.pathomation.com/"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">http://free.pathomation.com/</span></span><span style="mso-bookmark:_MailEndCompose"></span></a><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US">Thomas Melin<o:p></o:p></span></span></p>
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<p class="MsoNormal" style="line-height:11.25pt"><span style="mso-bookmark:_MailEndCompose"><span style="color:black"><img border="0" width="134" height="65" style="width:1.3958in;height:.677in" id="img510001" src="cid:image001.png@01D3C294.FE925E70" alt="cid:420a99d5-cdc7-4fe7-9a54-27e37712392d"></span></span><span style="mso-bookmark:_MailEndCompose"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-GB" style="font-family:"Arial",sans-serif">Thomas Melin<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-GB" style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#33CCCC">Senior Development Engineer<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-GB" style="font-size:9.0pt;font-family:"Arial",sans-serif">ContextVision AB,
<span style="color:black">Storgatan 24, 582 23 Linköping, Sweden<br>
Phone: +46 (0)70 606 85 56</span><o:p></o:p></span></span></p>
<p class="MsoNormal" style="line-height:11.25pt"><span style="mso-bookmark:_MailEndCompose"></span><a href="http://www.contextvision.com/"><span style="mso-bookmark:_MailEndCompose"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#009999">www.contextvision.com</span></span><span style="mso-bookmark:_MailEndCompose"></span></a><span style="mso-bookmark:_MailEndCompose"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:black">
<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">Från:</span></b><span lang="EN-US"> openslide-users [mailto:openslide-users-bounces+thomas.melin=contextvision.se@lists.andrew.cmu.edu]
<b>För </b>Luca Lianas<br>
<b>Skickat:</b> den 23 mars 2018 10:29<br>
<b>Till:</b> Gong, Qi * <Qi.Gong@fda.hhs.gov><br>
<b>Kopia:</b> openslide-users@lists.andrew.cmu.edu<br>
<b>Ämne:</b> Re: Could anyone give us a guide about how to use openslide to view WSI<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Hi Mr Gong and everyone else in the mailing list,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">I’m Luca Lianas and I work at the Healthcare Flows group of the CRS4, a research center in Italy.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">We’ve been working for a few years now on systems based on Digital Pathology images and, in particular, we developed a tool that can be considered as a plugin for Openmicroscopy’s OMERO (</span><a href="https://www.openmicroscopy.org/omero/"><span lang="EN-US">https://www.openmicroscopy.org/omero/</span></a><span lang="EN-US">)
that basically act as a DZI adapter for OME’s platform.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Our plugin, called ome_seadragon (</span><a href="https://www.openmicroscopy.org/omero/"><span lang="EN-US">https://www.openmicroscopy.org/omero/</span></a><span lang="EN-US">) uses both OMERO and OpenSlide and rendering
engine for the images and is based on the deepzoom project cited by David de Mena.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">The plugin has both the back-end engine to render images in DZI format and the front-end viewer, which is OpenSeadragon, packet as a Javascript library.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">The viewer has also drawing utilities developed by using Paper.js which make possible to the user to interact with the image and add 2D graphics on top of that as Regions of Interest.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">ome_seadragon is now part of a few projects that we are running over the years, one of them is a e-learning platform called CyTest and if you want to “take a look” to the platform and how the viewer has been integrated
with that you can read the publication on Research Gate </span><a href="https://www.researchgate.net/publication/305889225_CyTest_-_An_Innovative_Open-source_Platform_for_Training_and_Testing_in_Cythopathology"><span lang="EN-US">https://www.researchgate.net/publication/305889225_CyTest_-_An_Innovative_Open-source_Platform_for_Training_and_Testing_in_Cythopathology</span></a><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">I think that ome_seadragon could be considered as a good example on how to use OpenSlide to convert images in DZI format and how to integrate it with an online viewer with ROI marking capabilities.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">I hope that my two cents on the discussion were useful.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Luca Lianas<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">On 22 Mar 2018, at 17:30, David de Mena <</span><a href="mailto:david.mena.exts@juntadeandalucia.es"><span lang="EN-US">david.mena.exts@juntadeandalucia.es</span></a><span lang="EN-US">> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Hi Mr Gong:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">There is a python library base on openslide to create deepzoom images: </span><a href="https://github.com/openslide/openslide-python/blob/master/openslide/deepzoom.py"><span lang="EN-US">https://github.com/openslide/openslide-python/blob/master/openslide/deepzoom.py</span></a><span lang="EN-US"> Together
with a openseadragon (or Googlemaps) JavaScript library you can navigate in the image with a level,x,y. <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">In an European project called AIDPATH Public Health System of Andalusia have created a DICOM WSI converter/viewer based on this system. <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US">Best <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:13.8pt"><b><span lang="EN-US">David de Mena García</span></b><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">Responsable de Proyectos de Innovación TIC / ICT Innovation Project Manager</span></b><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Consejería de Salud de la Junta de Andalucía / Regional Ministry of Health<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US"> </span></b><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US"> </span></b><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">M </span><a href="tel:+34%20671%20565%20998"><span lang="EN-US">+34 671 565 998</span></a><span lang="EN-US"> | C<b> </b>76 59 98<o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:13.8pt"><span lang="EN-US">T </span><a href="tel:+34%20955%20402%20170"><span lang="EN-US">+34 955 402 170</span></a><span lang="EN-US"> |<b> </b>C<b> </b>37 91 70<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:10.0pt;line-height:13.8pt"><span lang="EN-US">Este correo electrónico y, en su caso, cualquier fichero anexo, contiene información confidencial exclusivamente dirigida a su(s) destinatario(s). Toda copia o divulgación
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US"><br>
El 22 mar 2018, a las 15:51, Gong, Qi * <</span><a href="mailto:Qi.Gong@fda.hhs.gov"><span lang="EN-US">Qi.Gong@fda.hhs.gov</span></a><span lang="EN-US">> escribió:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">Registration accuracy between whole slide images and glass slides in eeDAP workflow<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">_______________________________________________<br>
openslide-users mailing list<br>
</span><a href="mailto:openslide-users@lists.andrew.cmu.edu"><span lang="EN-US">openslide-users@lists.andrew.cmu.edu</span></a><span lang="EN-US"><br>
</span><a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users"><span lang="EN-US">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</span></a><span lang="EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:black">---<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:black">Luca Lianas<br>
Data Intensive Computing - Healthcare Flows<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="color:black">CRS4 - Centro di Ricerche, Sviluppo e Studi Superiori della Sardegna<br>
POLARIS, Edificio 1, 09010 PULA (CA - Italy)<o:p></o:p></span></p>
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<p class="MsoNormal"><a href="mailto:luca.lianas@crs4.it">Email: luca.lianas@crs4.it</a><span style="color:black"><o:p></o:p></span></p>
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