<div dir="ltr"><div><div><div><div>Hi Qi,<br><br></div>I don't know the schedule but I do know some very capable people are working on it so I expect it will not be too long.<br><br></div>For the interim, note that one of my colleagues has found that doing the following generates WSI CZI files that are quite manageable:<br>"I think I just found a better way to deal with large,
Axioscan-generated JPEG-XR images. If I simply select “save as with
options” in the Zen file menu, I can select “uncompressed” and also
eliminate some of the pyramid levels (1 to 3 or 1 to 4 works
fine). This reduces the file size by almost 10-fold, and the images
successfully import to OMERO (display settings still don’t transfer yet
though). I haven’t noticed a reduction in quality in the OMERO images."<br><br></div>Cheers,<br></div>- Damir<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 8, 2016 at 2:33 PM, Qi Gong <span dir="ltr"><<a href="mailto:qigong@gwmail.gwu.edu" target="_blank">qigong@gwmail.gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Damir,<div><br></div><div>Thank you very much. Do you know when will that version come? I will try uncompressed format. </div><div><br></div><div>Regards,</div><div>Qi </div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 8, 2016 at 5:27 PM, Damir Sudar <span dir="ltr"><<a href="mailto:dsudar@lbl.gov" target="_blank">dsudar@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi Qi,<br><br></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><br></div>- Damir<br></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Wed, Jun 8, 2016 at 2:00 PM, Qi Gong <span dir="ltr"><<a href="mailto:qigong@gwmail.gwu.edu" target="_blank">qigong@gwmail.gwu.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hello everyone,<div><br></div><div>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><div><br></div><div><div>>> WSI_data = bfGetReader('C:\000_whole_slides\WSIcziexample.czi');</div><div><br></div><div>Warning: *** Insufficient memory detected. ***</div><div>*** 352m found ***</div><div>*** 512m or greater is recommended ***</div><div>*** See <a href="http://www.mathworks.com/matlabcentral/answers/92813" target="_blank">http://www.mathworks.com/matlabcentral/answers/92813</a> ***</div><div>*** for instructions on increasing memory allocation. ***</div><div> </div><div>> In bfCheckJavaMemory (line 53)</div><div> In bfGetReader (line 47) </div><div>Error using bfGetReader (line 85)</div><div>Java exception occurred:</div><div>loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2936)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2908)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:557)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div><div><br></div><div><span style="white-space:pre-wrap"> </span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)</div><div><br></div><div>Regards,</div><div>Qi</div><span><font color="#888888"><div><br></div>-- <br><div data-smartmail="gmail_signature">mobile phone: <a href="tel:2024060862" value="+12024060862" target="_blank">2024060862</a></div>
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<br></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br><div data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Damir Sudar - Staff Scientist<br>Lawrence Berkeley National Laboratory<br>One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<br>T: <a href="tel:510%2F486-5346" value="+15104865346" target="_blank">510/486-5346</a> - F: <a href="tel:510%2F486-5586" value="+15104865586" target="_blank">510/486-5586</a> - E: <a href="mailto:DSudar@lbl.gov" target="_blank">DSudar@lbl.gov</a><br><br></div></div><div>Visiting Scientist, Oregon Health and Science University</div></div></div></div></div></div></div>
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<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div data-smartmail="gmail_signature">mobile phone: <a href="tel:2024060862" value="+12024060862" target="_blank">2024060862</a></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Damir Sudar - Staff Scientist<br>Lawrence Berkeley National Laboratory<br>One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<br>T: 510/486-5346 - F: 510/486-5586 - E: <a href="mailto:DSudar@lbl.gov" target="_blank">DSudar@lbl.gov</a><br><br></div></div><div>Visiting Scientist, Oregon Health and Science University</div></div></div></div></div></div></div>
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