<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Thomas,<br>
<br>
I'll be happy to provide hosting space if needed.<br>
<br>
Thanks.<br>
<br>
El 22/03/13 13:33, ROUSVOAL thomas escribió:<br>
</div>
<blockquote
cite="mid:B93B078EEFECC347815B65B015EB4608148E8F22@EXCHMBX-SRV2.chu-caen.fr"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.hoenzb
{mso-style-name:hoenzb;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">Hi guys,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">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
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">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
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">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
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US"><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
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US"><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"">
<a class="moz-txt-link-abbreviated" href="mailto:openslide-users-bounces+rousvoal-t=chu-caen.fr@lists.andrew.cmu.edu">openslide-users-bounces+rousvoal-t=chu-caen.fr@lists.andrew.cmu.edu</a>
[<a class="moz-txt-link-freetext" href="mailto: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</a>]
<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>
<div>
<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>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Sat, Mar 16, 2013 at 10:44 AM,
Mathieu Malaterre <<a moz-do-not-send="true"
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>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
On Sat, Mar 16, 2013 at 2:48 PM, David Gutman <<a
moz-do-not-send="true"
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>
</div>
<p class="MsoNormal">It's 'DICOM' uppercase, as any other
acronym<o:p></o:p></p>
<div>
<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>
</div>
<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>
</div>
<p class="MsoNormal"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<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>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
<br>
Email secured by Check Point <o:p></o:p></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
openslide-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a>
<a class="moz-txt-link-freetext" href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</a>
</pre>
</blockquote>
<br>
</body>
</html>