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Hi Qi,
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<div class="">These ratings are more an appreciation of our support of the file format and will</div>
<div class="">typically reflect the size/variety of our datasets, the availability of a specification</div>
<div class="">document...</div>
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<div class="">That being said, all WSI file formats listed in that table are expected to be readable</div>
<div class="">using Bio-Format. Known limitations like the unsupported JPEG-XR compression should</div>
<div class="">be described directly in the individual format page - see e.g.</div>
<div class="">
<div class=""><a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html" class="">http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html</a></div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<blockquote type="cite" class="">
<div class="">On 20 Jul 2016, at 19:36, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" class="">qigong@gwmail.gwu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello Damir,
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<div class="">I have one more question about available image format. On your website I find this link <a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html" class="">http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html</a>.</div>
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<div class="">There are a lot of image formats and several rating titles. I want to know if I want to load the WSI image to Matlab through Bioformat, I should focus on which title? And the rating should be higher than "fair" or "good"? Thank you.</div>
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<div class="">Regards,</div>
<div class="">Qi</div>
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<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Wed, Jun 8, 2016 at 5:27 PM, Damir Sudar <span dir="ltr" class="">
<<a href="mailto:dsudar@lbl.gov" target="_blank" class="">dsudar@lbl.gov</a>></span> wrote:<br class="">
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<div class="">Hi Qi,<br class="">
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</div>
In general CZI images, including WSI images, are supported by BioFormats and as you know, you need lots of memory allocated. However, internally JPEG-XR-compressed CZI images are currently not yet supported at all. This is expected to change in the near future.
Meanwhile, you can save the images in uncompressed format using Zeiss's ZEN application in order to read them with your application with BioFormats.<br class="">
<br class="">
</div>
- Damir<br class="">
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<div class="gmail_extra"><br class="">
<div class="gmail_quote">
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<div class="h5">On Wed, Jun 8, 2016 at 2:00 PM, Qi Gong <span dir="ltr" class="">
<<a href="mailto:qigong@gwmail.gwu.edu" target="_blank" class="">qigong@gwmail.gwu.edu</a>></span> wrote:<br class="">
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<div dir="ltr" class="">Hello everyone,
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<div class="">Sorry for bother. I want to know could I use Bio-Formats read .czi format WSI image in matlab? I could read in .svs and .ndpi formats now. When I used same code to read in .czi file, matlab gave me error. Thank you very much.</div>
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<div class="">>> WSI_data = bfGetReader('C:\000_whole_slides\WSIcziexample.czi');</div>
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<div class="">Warning: *** Insufficient memory detected. ***</div>
<div class="">*** 352m found ***</div>
<div class="">*** 512m or greater is recommended ***</div>
<div class="">*** See <a href="http://www.mathworks.com/matlabcentral/answers/92813" target="_blank" class="">
http://www.mathworks.com/matlabcentral/answers/92813</a> ***</div>
<div class="">*** for instructions on increasing memory allocation. ***</div>
<div class=""> </div>
<div class="">> In bfCheckJavaMemory (line 53)</div>
<div class=""> In bfGetReader (line 47) </div>
<div class="">Error using bfGetReader (line 85)</div>
<div class="">Java exception occurred:</div>
<div class="">loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported</div>
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</div>
<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2936)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2908)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:557)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
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<div class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)</div>
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<div class="">Regards,</div>
<div class="">Qi</div>
<span class=""><font color="#888888" class="">
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<div dir="ltr" class="">Damir Sudar - Staff Scientist<br class="">
Lawrence Berkeley National Laboratory<br class="">
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<br class="">
T: <a href="tel:510%2F486-5346" value="+15104865346" target="_blank" class="">510/486-5346</a> - F:
<a href="tel:510%2F486-5586" value="+15104865586" target="_blank" class="">510/486-5586</a> - E:
<a href="mailto:DSudar@lbl.gov" target="_blank" class="">DSudar@lbl.gov</a><br class="">
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<div class="">Visiting Scientist, Oregon Health and Science University</div>
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