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. <div><br></div><div><br></div><div><div>vips im_vips2tiff INPUT_SVS_FILE.svs OUTPUT.dzi.tif:jpeg:75,tile:256x256,pyramid,,,,8</div>
<div><br></div><div><br></div><div>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...</div>
<div><br></div><div>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.</div>
<div><br></div><div><br></div><div><br></div><div><br></div><br><div class="gmail_quote">On Mon, Jun 4, 2012 at 5:09 PM, Benjamin Gilbert <span dir="ltr"><<a href="mailto:bgilbert@cs.cmu.edu" target="_blank">bgilbert@cs.cmu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On 06/04/2012 08:35 AM, M. Satyanarayanan wrote:<br>
> I would like to thank you for your efforts in developing and maintaining a<br>
> project such as OpenSlide. It has been a real lifesaver for us and has<br>
> allowed us to do some really cool things over the past year.<br>
<br>
</div>Glad to hear it!<br>
<div class="im"><br>
> We were recently able to recompile the OpenSlide library in a 64-bit<br>
> version (which was a challenge with all the dependencies). Would you be<br>
> interested in hosting this 64-bit version of the library and perhaps<br>
> benchmarking it for speed?<br>
<br>
</div>I assume this is a native Windows build? I suspect what the list would<br>
find more useful than the binaries is a set of instructions for the<br>
build process you used.<br>
<div class="im"><br>
> * Our current generation of the 3DHistech scanner generates MRXS files<br>
> that cannot be read by OpenSlide. Examples of these files are at<br>
> <a href="http://www.histogenex.com/agelos/mrxs/problem_mrxs.zip" target="_blank">http://www.histogenex.com/agelos/mrxs/problem_mrxs.zip</a><br>
<br>
</div>This is a known problem. The Git repository contains a patch that<br>
allows these slides to be opened, but the slide tile overlaps are not<br>
correct. This issue is being tracked at<br>
<<a href="https://github.com/openslide/openslide/issues/92" target="_blank">https://github.com/openslide/openslide/issues/92</a>>.<br>
<div class="im"><br>
> * Why did you choose the OpenSeadragon viewer and not some other platform<br>
> such as e.g. Zoomify or OpenLayers?<br>
<br>
</div>Zoomify is a proprietary product. As to OpenLayers, we were originally<br>
thinking in terms of zoomable image viewers rather than map viewers.<br>
<br>
Although we currently use OpenSeadragon for our demo applications,<br>
there's nothing requiring you to use OpenSeadragon. You should be able<br>
to use the OpenSlide API to implement a tiler for the image viewer of<br>
your choice.<br>
<br>
(OpenSeadragon appears to be unmaintained, so an interface to other<br>
viewers might indeed be useful.)<br>
<div class="im"><br>
> * Do you have plans to incorporate the ZVI format as well in OpenSlide?<br>
<br>
</div>Not at present, but contributions are welcome.<br>
<div class="im"><br>
> * Do you have experience with Leica's BigTIFF format and how does it<br>
> differ from the currently supported TIFF formats in OpenSlide?<br>
<br>
</div>Nope, sorry.<br>
<br>
<br>
Unfortunately, we don't have the resources to promptly implement all of<br>
the features we (and our users) would like. If there's a feature that's<br>
important to you, please consider developing it yourself and<br>
contributing it to OpenSlide; after all, that's the point of a<br>
community-driven project! I would be happy to provide design advice,<br>
answer questions, and review code.<br>
<span class="HOEnZb"><font color="#888888"><br>
--Benjamin Gilbert<br>
</font></span><div class="HOEnZb"><div class="h5">_______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>David A Gutman, M.D. Ph.D.<br>Assistant Professor of Biomedical Informatics<br>Senior Research Scientist, Center for Comprehensive Informatics<br>Emory University School of Medicine<br>
</div>