VIPS / SVS

[Niels Werner Mortensen]

Dear All,


Another approach in case you're interested :)

For the University in Copenhagen I´m heading a project for a Virtual Microscopy Service (VIRMIK). VIRMIK uses the PathXL application as the "integration" platform and we accept slides from the Pannoramic MIDI slide scanner (MRXS) and from the Olympus Dost Slide scanner (VSI). The internal slide format in PathXL is Aperios SVS. In the very near future we will accept slides from the new Axio Scan from Zeiss (due in October) and later maybe for the Hammamatsu NanoZoomer, but this is still un-decided.

I had the main vendor = PathXL Ltd. In Belfast create the MRXS/SVS converter and why they did not take advantage of the openslide forum I honestly don't know/understand!


Best regards,

Niels Werner Mortensen
IT Project Manager

Department of Biomedical Sciences
Faculty Of Health Sciences
University of Copenhagen
Blegdamsvej 3B,
DK-2200 Copenhagen N
Denmark

TEL +45 35327457
DIR +45 28757520
MOB +45 28757520
FAX +45 35327537
Room 12.3.14
nwm at sund.ku.dk
bmi.ku.dk

[C:\Users\fcp486\AppData\Roaming\Microsoft\Signatures\logo-en.gif]


-----Original Message-----
From: openslide-users-bounces+nwm=sund.ku.dk at lists.andrew.cmu.edu [mailto:openslide-users-bounces+nwm=sund.ku.dk at lists.andrew.cmu.edu] On Behalf Of Priv.-Doz. Dr. M. Weihrauch
Sent: 22. september 2012 00:17
To: openslide-users at lists.andrew.cmu.edu
Subject: VIPS / SVS

Dear All:

I am a hematologist from the Germany and for appr. 6 months I am trying to establish virtual microscopy for our hematology dept.
The whole Aperio/Openslide/ python script has robbed me as a Windows user some nerves...
finally we somehow got the NYU python script working for converting SVS slides to google-tiles, but it was terribly slow and after some Ubuntu update with one library different now, everything fails again (libtiff?).

However, I was happy to see one post about using VIPS to directly create DeepZoom tiles. But: I found 2 bugs / problems with the dzsave-option of Windows vips 7.30.1 vips.exe file:

1. It only works on large TIF that I have exported from Aperio SVS  with Imagescope and on the files that I have converted to SVS(JPEG) with imagescope. However, if I want to use the original SVS (with internal JPEG2000), it only produces black tiles.

2. It does not make the tiles until 1px in zoom level 0, but stops around zoom level 9 or 10 depending on the size. The last zoom level (e.
g. 9) only contains half of the image. There was no error message by the vips.exe. Thus, when you run seadragon, you only see half of the image.
When you zoom in, it displays the full image. I checked on the directories and there are really half of the tiles missing.

I used something like:

vips dzsave --<inputimage.tif (or svs(jpg))> --outdir --overlap=0
--tile-width=256 --tile-height=256

3. One important question: how can I set a JPEG compression level?

4. Under which license is the entire library?

Thanks so much for your great work!

Martin Weihrauch

_______________________________________________
openslide-users mailing list
openslide-users at lists.andrew.cmu.edu<mailto:openslide-users at lists.andrew.cmu.edu>
https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20120922/abbad99d/attachment.html