<div dir="ltr">Hello Damir,<div><br></div><div>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">http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html</a>.</div><div><br></div><div>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><div><br></div><div>Regards,</div><div>Qi</div><div><br></div><div><br></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 class="h5">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 class="h5"><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 class="HOEnZb"><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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