Fwd: OpenSlide library inquiry
dagutman at gmail.com
Tue Jun 5 07:45:45 EDT 2012
aaah ok--- so I have to just make sure when I build VIPS from source I
compile against openslide as well--- I think last time I compiled it I was
building against the latest version of libtiff as well--- how does VIPS
"know" which library to use th read the JPEG2000 encoded tiff's or is there
some search hierarchy if it finds an encoding library X won't handle, it
will go to library Y?
On Mon, Jun 4, 2012 at 11:06 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu>wrote:
> On 06/04/2012 07:39 PM, David Gutman wrote:
>> Ben--- I've been using vips to transcode raw SVS files into pyramidal
>> tiff files... and it works as long as the images are not JPEG2000 encoded.
>> vips im_vips2tiff INPUT_SVS_FILE.svs
>> Basically the above command tells VIPS to transcode the original SVS
>> file (layer 0) into a pyramidal tiff at 75% quality as a jpeg, at
>> 256x256 tiles--- the "8" at the end tells it to save it as a BIGTIFF
>> image. I use the dzi.tif extension to remind me it's a deep
>> zoom/pyramidal tiff file...
> Actually, Deep Zoom is a particular file format, unrelated to TIFF.
> Do you think it would be possible to use VIPS/OpenSlide together to
>> accomplish the same thing in a single python script? With the recent
>> integration/support of VIPS and OpenSlide that I saw I was hoping this
>> possible, but haven't delved into the details.
> I haven't looked at the VIPS Python bindings, but if you have VIPS >=
> 7.28.3 linked against OpenSlide, it should be straightforward. You can
> also do this directly from the VIPS command line. The obvious approach
> with "vips tiffsave" does *not* work, because the TIFF writer gets confused
> by the fourth (alpha) channel returned by OpenSlide. But you can use
> vips im_extract_bands INPUT.svs \
> OUTPUT.tif:jpeg:75,tile:**256x256,pyramid,,,,8 0 3
> --Benjamin Gilbert
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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