<div dir="ltr">Hello Sebastien,<div><br></div><div>I got it. Thank you very much.</div><div><br></div><div>Regards,</div><div>Qi</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jul 25, 2016 at 11:00 AM, Sebastien Besson (Staff) <span dir="ltr"><<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Qi,
<div><br>
</div>
<div>
<div>These ratings are more an appreciation of our support of the file format and will</div>
<div>typically reflect the size/variety of our datasets, the availability of a specification</div>
<div>document...</div>
</div>
<div><br>
</div>
<div>That being said, all WSI file formats listed in that table are expected to be readable</div>
<div>using Bio-Format. Known limitations like the unsupported JPEG-XR compression should</div>
<div>be described directly in the individual format page - see e.g.</div>
<div>
<div><a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html" target="_blank">http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html</a></div>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div><div><div class="h5">
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 20 Jul 2016, at 19:36, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" target="_blank">qigong@gwmail.gwu.edu</a>> wrote:</div>
<br>
<div>
<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" target="_blank">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>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>
</font></span></div>
</div>
<br>
</div>
</div>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<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>
</font></span></div>
<br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
</blockquote>
</div>
<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>
</div>
</div>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
</div>
</blockquote>
</div>
<br>
</div>
<br>
</div></div><span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
<br>_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">mobile phone: 2024060862</div>
</div>