VIPS / SVS

[Priv.-Doz. Dr. M. Weihrauch]

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