DICOM supplement 145 inquiry

[ROUSVOAL thomas]

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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