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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[Apparently I didn’t send this to the list first time… I’m really interested in others opinions on OME-TIFF too!]</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">My 2c…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We use Aperio .svs as the native format for writing output images in our digital pathology image analysis system (</span><a href="http://www.medicalimagemanager.com"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">http://www.medicalimagemanager.com</span></a><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
if were advertising </span><span style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">). This is a (reasonably) well described tiled tiff format supporting jpeg
and jpeg2000 tiles, which is reasonably easy to write with open source libtiff (+openjpeg for jpeg2000). You also need BigTIFF support for larger files (but I can’t really see a way round that one), and it isn’t readable by standard tiff viewers (again if
you are talking a tiled format I can’t see a way round that one either). Obviously the main advantage is it is supported by OpenSlide already (as well as Bioformats).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have no real issues with svs, but I was also thinking of looking at OME-TIFF too (I like the fact the format is openly described, although a bit too flexible
maybe). It isn’t widely used in digital pathology though, but is quite widely used in other microscopy areas. I’m interested in other’s opinions if it will ever be a major format in digital microscopy?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">One thing about bio-formats that put me off is that it has a tangle of different licences. Some features require a commercial licence for commercial use (Open
Microscopy isn’t quite as open as OpenSlide in that respect). It’s also written in Java, and while there are bindings for other languages (e.g. c++ binding in ITK) it does complicate things (i.e. Java needs to be installed an configured) if you aren’t using
Java. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Derek<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openslide-users [<a href="mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk@lists.andrew.cmu.edu">mailto:openslide-users-bounces+d.r.magee=leeds.ac.uk@lists.andrew.cmu.edu</a>]
<b>On Behalf Of </b>Dmitry Fedorov via openslide-users<br>
<b>Sent:</b> 12 January 2016 17:22<br>
<b>To:</b> Andreas Schmid<br>
<b>Cc:</b> <a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><br>
<b>Subject:</b> Re: OME-TIFF<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You could use libbioimage <<a href="https://bitbucket.org/dimin/bioimageconvert">https://bitbucket.org/dimin/bioimageconvert</a>> alongside OpenSlide to achieve full support for OME-TIFF and WSI. In fact it supports pyramidal and tiled
OME-TIFF and OME-BigTIFF that are not strictly standardised. It also supports other formats not yet available in OpenSlide, like tiled JPEG-2000 (this will get a lot better with the next openjpeg library version). <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Libbioimage is a complimentary library for OpenSlide since it was designed to support multi-dimensional and multi-channel fluorescence imagery. In our system BisQue (management and analysis system) we use openslide for WSI and libbioimage
for OME-TIFF for very large images daily. Finally, I decided to integrate OpenSlide into libbioimage as one of the decoders and this should be finished for the next version. I also hope to incorporate OpenSlide extensions like DICOM-WSI from Mathieu Malaterre
and have started writing a CZI importer supporting fluorescence. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Although I use OME-TIFF as our main interchange format and do like it, we have encountered a few problems in more than 10 years of use, I'll try to list those for your consideration.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) Really large images require BigTIFF packaging and thus become unreadable by most programs supporting TIFF.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2) Pyramidal-tiled OME-TIFF is not standardised. I prefer sub-directory based approach (similar to Photoshop's pyramid) myself but implemented support for other cases I know.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">3) Every channel plane is stored in a separate directory making it a bit slower to read all the channels since one must change directory several times for every tile.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">4) TIFFs with many directories become very slow to read since one must traverse the whole file until the desired directory is reached. I've worked with very large 4D OME-TIFFs with hundreds of thousands of directories. Although libbioimage
patched libtiff with a few optimizations for this case it is still a real problem. The solution to this is unfortunately a multi-file solution where each 3D block is stored as a separate OME-TIFF file.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">5) OME-TIFF metadata model is quite rigid and designed for a specific use. It does provide a flat name-value list for extended information but it is very verbose and too simple to store a large amount of complex information. Thousands of
tags will make that list very slow to parse. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Folks at OME consortium published a paper proposing to use an HDF-5 based format for lifesciences. Although it sounds like a great idea there's no standard definition for it yet. Many companies are using HDF5 based formats for a long time
but they are all proprietary, for example Imaris ims5. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal">dmitry<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Jan 12, 2016 at 2:46 AM, Andreas Schmid via openslide-users <<a href="mailto:openslide-users@lists.andrew.cmu.edu" target="_blank">openslide-users@lists.andrew.cmu.edu</a>> wrote:<o:p></o:p></p>
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<p style="margin:0cm;margin-bottom:.0001pt"><b><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">Thoughts on OME-TIFF as an OpenSlide Format</span></b><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">Actually our company saves the WSI images as an zipped deepzoom pyramid simular to Martin Weihrauchs Smart Zoom Image approach. Unfortunately this format
lacks third party support and likely ever will and suffers from the detriments of a non-image format (Like viewing it in any other tiff supported software when it is not too large).</span><o:p></o:p></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">We took some research in the past weeks and considering to switch to a tiff-based WSI format but we are not strigency interested to do our's own thing
to be just another one who sheers off from a standardized WSI format.</span><o:p></o:p></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">So we kept an wary eye on the OME-TIFF format.</span><o:p></o:p></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">What do you think? Is OME-TIFF a canditate for beeing an openslide format too?</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.5pt;font-family:"Arial","sans-serif"">How do you think will OME develop in the future?</span><o:p></o:p></p>
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_______________________________________________<br>
openslide-users mailing list<br>
<a href="mailto:openslide-users@lists.andrew.cmu.edu">openslide-users@lists.andrew.cmu.edu</a><br>
<a href="https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users" target="_blank">https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users</a><o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">__________________________________<br>
<br>
Dmitry Fedorov Levit <<a href="mailto:dima@dimin.net" target="_blank">dima@dimin.net</a>><br>
Web: <a href="http://www.dimin.net/" target="_blank">http://www.dimin.net/</a><br>
__________________________________<br>
<br>
Center for Bio-Image Informatics:<br>
<<a href="http://www.bioimage.ucsb.edu/" target="_blank">http://www.bioimage.ucsb.edu/</a>><br>
<br>
Vision Research Lab, Electrical and Computer Engineering:<br>
<<a href="http://vision.ece.ucsb.edu/" target="_blank">http://vision.ece.ucsb.edu/</a>><br>
<br>
University of California, Santa Barbara<br>
_________________________________<o:p></o:p></p>
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