Fwd: OpenSlide library inquiry

David Gutman dagutman at gmail.com
Mon Jun 4 19:39:04 EDT 2012

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...

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.

On Mon, Jun 4, 2012 at 5:09 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu>wrote:

> On 06/04/2012 08:35 AM, M. Satyanarayanan wrote:
> > I would like to thank you for your efforts in developing and maintaining
> a
> > project such as OpenSlide. It has been a real lifesaver for us and has
> > allowed us to do some really cool things over the past year.
> Glad to hear it!
> > We were recently able to recompile the OpenSlide library in a 64-bit
> > version (which was a challenge with all the dependencies). Would you be
> > interested in hosting this 64-bit version of the library and perhaps
> > benchmarking it for speed?
> I assume this is a native Windows build?  I suspect what the list would
> find more useful than the binaries is a set of instructions for the
> build process you used.
> > * Our current generation of the 3DHistech scanner generates MRXS files
> > that cannot be read by OpenSlide. Examples of these files are at
> > http://www.histogenex.com/agelos/mrxs/problem_mrxs.zip
> This is a known problem.  The Git repository contains a patch that
> allows these slides to be opened, but the slide tile overlaps are not
> correct.  This issue is being tracked at
> <https://github.com/openslide/openslide/issues/92>.
> > * Why did you choose the OpenSeadragon viewer and not some other platform
> > such as e.g. Zoomify or OpenLayers?
> Zoomify is a proprietary product.  As to OpenLayers, we were originally
> thinking in terms of zoomable image viewers rather than map viewers.
> Although we currently use OpenSeadragon for our demo applications,
> there's nothing requiring you to use OpenSeadragon.  You should be able
> to use the OpenSlide API to implement a tiler for the image viewer of
> your choice.
> (OpenSeadragon appears to be unmaintained, so an interface to other
> viewers might indeed be useful.)
> > * Do you have plans to incorporate the ZVI format as well in OpenSlide?
> Not at present, but contributions are welcome.
> > * Do you have experience with Leica's BigTIFF format and how does it
> > differ from the currently supported TIFF formats in OpenSlide?
> Nope, sorry.
> Unfortunately, we don't have the resources to promptly implement all of
> the features we (and our users) would like.  If there's a feature that's
> important to you, please consider developing it yourself and
> contributing it to OpenSlide; after all, that's the point of a
> community-driven project!  I would be happy to provide design advice,
> answer questions, and review code.
> --Benjamin Gilbert
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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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