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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi guys,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m using the SCN400 Leica scanner, and it can natively product some natively DICOM145 encoded WSI image files since a few months.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’m not using it routinely yet because I need to adapt some quality check algorithms, but at least I can provide you some “leica 145” example files.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The things is my scanner is not connected to the LSI so the identification metadata will contain at most the barcode data.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Thomas Rousvoal,</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Microscopie Virtuelle,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Groupe MESOPATH,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">CHU de CAEN<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Avenue de la Côte de Nacre<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">CS 30001<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">14033 CAEN CEDEX 9<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">02.31.06.48.12</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openslide-users-bounces+rousvoal-t=chu-caen.fr@lists.andrew.cmu.edu [mailto:openslide-users-bounces+rousvoal-t=chu-caen.fr@lists.andrew.cmu.edu]
<b>De la part de</b> David Gutman<br>
<b>Envoyé :</b> samedi 16 mars 2013 15:57<br>
<b>À :</b> Mathieu Malaterre<br>
<b>Cc :</b> OpenSlide Users<br>
<b>Objet :</b> Re: DICOM supplement 145 inquiry<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Mathieu-- agreed. My experience in the DICOM world with radiology images is that converting from some format to DICOM is extremely extremely challenging as you point out, which is likely even worse for the whole slide images. Although
as Yves points out, it's somewhat of a chicken and egg issue if there are no files already available for someone to try and develop a library against, nor any vendor that can generate files in the proper format. <o:p></o:p></p>
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<p class="MsoNormal">While it sounds like it would be extremely resource intensive to get a legacy format-->DICOM sup145 converter developed, but would be extremely interesting. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Is the expectation that the vendors themselves would be developing the libraries / functionality so images can be saved directly as a DICOM WSI image? And are any vendors working on that?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Having spent several years dealing with various oddities of vendor specific formats, it would be interesting to know what the timeline (if any) of that functionality being developed.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Sat, Mar 16, 2013 at 10:44 AM, Mathieu Malaterre <<a href="mailto:mathieu.malaterre@gmail.com" target="_blank">mathieu.malaterre@gmail.com</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi David,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
On Sat, Mar 16, 2013 at 2:48 PM, David Gutman <<a href="mailto:dagutman@gmail.com">dagutman@gmail.com</a>> wrote:<br>
> Yves-- I am familiar at least at some high level with the Dicom standard--<br>
> although as you point out it's a standard without a way to read or write<br>
> images, and no images to even test on!<o:p></o:p></p>
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<p class="MsoNormal">It's 'DICOM' uppercase, as any other acronym<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
> I am not sure how well the standard maps to the OMETIFF format-- but that<br>
> would likely be the easiest way to go. I routinely convert images I scan<br>
> on either an Aperio machine or an Olympus Nanozoomer into "just a tiff"....<br>
> so presumably we could generate a tiff and then "reformat" it so that it<br>
> meets the DICOM standard, including adding all of the necessary metadata.<br>
> I don't have much experience with the library directly (I hate editing<br>
> Java)... but since it's open source, and the properties and data model are<br>
> fairly well developed, it would be a template to hack onto the current OMERO<br>
> XML model and make it DICOM friendly...<o:p></o:p></p>
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<p class="MsoNormal">As explained by Yves, Sup 145 clearly specify all of that. Going to<br>
OME-TIFF as an intermediate steps, will only make the work actually<br>
even harder.<br>
Finally some slides do not have the complete image at full resolution,<br>
so you cannot simply 'drop' the intermediate levels, again Sup 145<br>
specify that.<br>
<br>
2cts<br>
<span class="hoenzb"><span style="color:#888888">--</span></span><span style="color:#888888"><br>
<span class="hoenzb">Mathieu</span></span><o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <br>
David A Gutman, M.D. Ph.D.<br>
Assistant Professor of Biomedical Informatics<br>
Senior Research Scientist, Center for Comprehensive Informatics<br>
Emory University School of Medicine <o:p></o:p></p>
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Email secured by Check Point <o:p></o:p></p>
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