Dicom sup.145 Leica files

[Mathieu Malaterre]

Hi everyone,

  First thing first: THANK YOU for sharing those DICOM/WSI. This is
very much appreciated.

  I will not comment on the LEICA/SCN files themself, I do not have
the background to comment on those.

  However, the DICOM/WSI are a little tricky to read. I have pushed a
patch in GDCM to handle them:

https://sourceforge.net/p/gdcm/gdcm/ci/9ed258dcdfbf430fc5080d96a528cfc990924053/

  If you get GDCM from either the release and/or the master branch
you'll be able to run:

$ gdcmconv CDCAB791/CDCAB791/4D47418B/CDCAB790 /tmp/clean.dcm

And then process 'clean.dcm' with your favorite DICOM toolkit. With
GDCM you'll be able to split the DICOM/WSI into its individual JPEG
streams. Eg:

$ gdcmraw -S -i /tmp/clean.dcm -o /tmp/wsi/thejpeg --pattern %03d.jpg

and thus:

$ file /tmp/wsi/thejpeg000.jpg
/tmp/wsi/thejpeg000.jpg: JPEG image data, JFIF standard 1.02, comment:
"Intel(R) IPP JPEG encoder [7.0.1032] - Apr 18 2011"

Some jpg looks corrupted to me. Eg for
CDCAB791/CDCAB791/4D47418B/CDCAB790, gdcmraw will extract:

- /tmp/wsi/thejpeg059.jpg
- /tmp/wsi/thejpeg082.jpg
- /tmp/wsi/thejpeg111.jpg
...

I have pushed one here:

http://gdcm.sourceforge.net/thingies/thejpeg082.jpg

2cts

On Mon, Mar 25, 2013 at 7:54 PM, Alvaro Gonzalez <agonzalez at kanteron.com> wrote:
> Good evening,
>
> Thanks to the help of Thomas Rousvoal, who uses a Leica SCN400, we have a
> pair of slides scanned both in SCN and "Leica DICOM 145" (I'll name it that
> way as I still don't know how near to the DICOM specs is) format.
>
> You can download them from:
>
> http://dicom.gonzalezcrespo.es/leica/
>
> The DICOM format came as a directory with several files, and the scn as one
> file. I compressed each one individually as a tar.gz file. I don't think
> you'll have problems with that format as most OS and compression software
> will deal correctly with it. If you are on windows and have any problem
> uncompressing them, I recommend you 7-Zip, it's an open source nice
> substitute for your regular WinZIP or WinRAR tools.
>
> Once uncompressed, I quote Thomas himself:
>
> To open those DICOM, install the viewer, in the open file message box,
> select the DICOM instead of scn, and select the DICOMDIR file in the first
> level of the directory.
> On the smallest slide, One area is scanned at 20x, In the other, one area is
> scanned at 20x, and another at 40x.
>
> Thanks all, hope it's helpful for everybody.
>
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>



-- 
Mathieu