DICOM supplement 145 inquiry

[Alvaro Gonzalez]

Hi Thomas,

I'll be happy to provide hosting space if needed.

Thanks.

El 22/03/13 13:33, ROUSVOAL thomas escribió:
>
> Hi guys,
>
> I'm using the SCN400 Leica scanner, and it can natively product some 
> natively DICOM145 encoded WSI image files since a few months.
>
> 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.
>
> The things is my scanner is not connected to the LSI so the 
> identification metadata will contain at most the barcode data.
>
> Regards,
>
> *Thomas Rousvoal,*
>
> Microscopie Virtuelle,
>
> Groupe MESOPATH,
>
> CHU de CAEN
>
> Avenue de la Côte de Nacre
>
> CS 30001
>
> 14033 CAEN CEDEX 9
>
> 02.31.06.48.12
>
> *De :*openslide-users-bounces+rousvoal-t=chu-caen.fr at lists.andrew.cmu.edu 
> [mailto:openslide-users-bounces+rousvoal-t=chu-caen.fr at lists.andrew.cmu.edu] 
> *De la part de* David Gutman
> *Envoyé :* samedi 16 mars 2013 15:57
> *À :* Mathieu Malaterre
> *Cc :* OpenSlide Users
> *Objet :* Re: DICOM supplement 145 inquiry
>
> 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.
>
> While it sounds like it would be extremely resource intensive to get a 
> legacy format-->DICOM sup145 converter developed, but would be 
> extremely interesting.
>
> 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?
>
> 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.
>
> On Sat, Mar 16, 2013 at 10:44 AM, Mathieu Malaterre 
> <mathieu.malaterre at gmail.com <mailto:mathieu.malaterre at gmail.com>> wrote:
>
> Hi David,
>
>
> On Sat, Mar 16, 2013 at 2:48 PM, David Gutman <dagutman at gmail.com 
> <mailto:dagutman at gmail.com>> wrote:
> > Yves-- I am familiar at least at some high level with the Dicom 
> standard--
> > although as you point out it's a standard without a way to read or write
> > images, and no images to even test on!
>
> It's 'DICOM' uppercase, as any other acronym
>
>
> > I am not sure how well the standard maps to the OMETIFF format-- but 
> that
> > would likely be the easiest way to go.  I routinely convert images I 
> scan
> > on either an Aperio machine or an Olympus Nanozoomer into "just a 
> tiff"....
> > so presumably we could generate a tiff and then "reformat" it so that it
> > meets the DICOM standard, including adding all of the necessary 
> metadata.
> > I don't have much experience with the library directly (I hate editing
> > Java)... but since it's open source, and the properties and data 
> model are
> > fairly well developed, it would be a template to hack onto the 
> current OMERO
> > XML model and make it DICOM friendly...
>
> As explained by Yves, Sup 145 clearly specify all of that. Going to
> OME-TIFF as an intermediate steps, will only make the work actually
> even harder.
> Finally some slides do not have the complete image at full resolution,
> so you cannot simply 'drop' the intermediate levels, again Sup 145
> specify that.
>
> 2cts
> --
> Mathieu
>
>
>
> -- 
> David A Gutman, M.D. Ph.D.
> Assistant Professor of Biomedical Informatics
> Senior Research Scientist, Center for Comprehensive Informatics
> Emory University School of Medicine
>
>
>
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>
>
>
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