<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ji,<div><br></div><div>Thanks for the extra information.</div><div> I've added it to the ticket at <a href="http://trac.openmicroscopy.org/ome/ticket/12885">http://trac.openmicroscopy.org/ome/ticket/12885</a>.</div><div>It won't be me fixing that bug, but when it is worked on you may be contacted for more info if we need it.</div><div><br></div><div> Thanks,</div><div><br></div><div> Will.</div><div><br></div><div><br><div><div>On 17 May 2015, at 13:33, Tang Ji <<a href="mailto:tangji0318@foxmail.com">tangji0318@foxmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Will,</div><div>Thanks for your help.</div><div>The interesting thing is that when there are several other .czi files under a folder, the error will recur. You can try to open a .czi file after you unzip the attachment, and then you'll get what I find.</div><div>I tested several versions of bioformats, and I found that the error exists from version 5.0.7 to 5.1.1. However, version 5.0.6 to 5.1.0-m3 is fine.</div><div>I hope the information will make me understood. Thanks again.</div><div><br></div><div>Ji</div><div>May 17, 2015</div><div><div><br></div><div><br></div><div style="font-size: 12px;font-family: Arial Narrow;padding:2px 0 2px 0;">------------------ Original ------------------</div><div style="font-size: 12px;background:#efefef;padding:8px;"><div><b>From: </b> "ome-users-request";<<a href="mailto:ome-users-request@lists.openmicroscopy.org.uk">ome-users-request@lists.openmicroscopy.org.uk</a>>;</div><div><b>Date: </b> Fri, May 15, 2015 05:51 PM</div><div><b>To: </b> "ome-users"<<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>>; <wbr></div><div></div><div><b>Subject: </b> ome-users Digest, Vol 122, Issue 17</div></div><div><br></div>Send ome-users mailing list submissions to<br> <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a href="mailto:ome-users-request@lists.openmicroscopy.org.uk">ome-users-request@lists.openmicroscopy.org.uk</a><br><br>You can reach the person managing the list at<br> <a href="mailto:ome-users-owner@lists.openmicroscopy.org.uk">ome-users-owner@lists.openmicroscopy.org.uk</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of ome-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Error to Open .czi File (William Moore)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 15 May 2015 10:51:23 +0100<br>From: William Moore <<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</a>><br>To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>Subject: Re: [ome-users] Error to Open .czi File<br>Message-ID:<br> <5A6720B2-23AB-4433-<a href="mailto:B56E-A7E3014CDC1E@lifesci.dundee.ac.uk">B56E-A7E3014CDC1E@lifesci.dundee.ac.uk</a>><br>Content-Type: text/plain; charset="windows-1252"<br><br>Hi Ji,<br><br>I tried opening with an updated Fiji (Bio-formats 5.1.1 and I see the same as you.<br>It looks like this is actually a 16-bit image that only contains 8-bit data.<br>The Original Metadata has:<br>BitsPerPixel 8<br>PixelType uint16<br><br>Bio-formats is reading the BitsPerPixel incorrectly, since it's setting the "SignificantBits" attribute to 16 (see screenshot).<br>I've created a ticket to fix this bug: <a href="https://trac.openmicroscopy.org/ome/ticket/12885">https://trac.openmicroscopy.org/ome/ticket/12885</a><br><br><br>Downloading the bioformats package from <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.1/">http://downloads.openmicroscopy.org/bio-formats/5.1.1/</a> and running<br>java -jar bioformats_package.jar ZEN\ 2\ Blue\ 8bit.czi<br>Seemed to work fine for me.<br>The Show Metadata option gave me this (showing SizeC = 1 and SizeT = 1).<br><br><Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.09999999999999999" PhysicalSizeY="0.09999999999999999" SignificantBits="16" SizeC="1" SizeT="1" SizeX="256" SizeY="256" SizeZ="1" Type="uint16"><br><br><br>Downloading the command line tools from the above url, and running<br><br>$ ./showinf ZEN\ 2\ Blue\ 8bit.czi<br><br>seemed to open the image fine. With?<br><br>Filename = /Users/wmoore/Documents/ZEN 2 Blue 8bit.czi<br>Series count = 1<br>Series #0 :<br> Image count = 1<br> RGB = false (1) <br> Interleaved = false<br> Indexed = true (false color)<br> Width = 256<br> Height = 256<br> SizeZ = 1<br> SizeT = 1<br> SizeC = 1<br> Thumbnail size = 128 x 128<br> Endianness = intel (little)<br> Dimension order = XYCZT (certain)<br> Pixel type = uint16<br> Valid bits per pixel = 8<br> Metadata complete = false<br> Thumbnail series = false<br> -----<br> Plane #0 <=> Z 0, C 0, T 0<br><br><br>Reading pixel data (0-0)<br> ************ no LUT for plane #0 ************<br> Read 1/1 planes (100%)<br>[done]<br>0.121s elapsed (121.0ms per plane)<br><br>Launching image viewer<br>?.<br><br><br>Are these the exact same jars that you downloaded?<br>I'm afraid I can't reproduce the problems you're having here and can only suggest you try again.<br><br> Hope you can get this working.<br>If it still fails to open, please send us any error messages or other info that might help to fix this.<br><br> Regards,<br><br> Will.<br><br><br><br><br><br><br>On 15 May 2015, at 07:05, "Tang Ji" <<a href="mailto:tangji0318@foxmail.com">tangji0318@foxmail.com</a>> wrote:<br><br>> Dear,<br>> I have a problem to use bioformats. I've updated my bioformats to its latest version 5.1.1. However, when I tried to open my .czi file (1st attachment) in ImageJ, it shows that it's a 16-bit image as follows. However, the original file is 8-bit image.<br>> <3006CB03@F490172D.BD8C5555><br>> <br>> Then I tried to open the .czi file with upgraded Fiji, but it fails completely.<br>> <2803D008@F490172D.BD8C5555><br>> <br>> What's worse, when I use command "java -jar bioformats_package_5.1.1.jar" to open the file, it shows that it contains 2 Z and 2 time points. However, it's only a 1-Z and 1-T image.<br>> <290ACF05@F490172D.BD8C5555><br>> <br>> Finally, if I use command "java -jar loci_tools.jar", I even cannot open the file.<br>> I'll really appreciate you if you know how to solve the problem. Thanks.<br>> <br>> Ji<br>> May 15, 2015<br>> <290ACF05@F490172D.BD8C5555><2803D008@F490172D.BD8C5555><3006CB03@F490172D.BD8C5555><ZEN 2 Blue 8bit.czi>_______________________________________________<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">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150515/62f4239b/attachment.html">http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150515/62f4239b/attachment.html</a>><br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: Screen Shot 2015-05-15 at 10.14.09.png<br>Type: image/png<br>Size: 239155 bytes<br>Desc: not available<br>URL: <<a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150515/62f4239b/attachment.png">http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150515/62f4239b/attachment.png</a>><br><br>------------------------------<br><br>Subject: Digest Footer<br><br>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br><br>------------------------------<br><br>End of ome-users Digest, Vol 122, Issue 17<br>******************************************<br></div><span><ZEN Test Sample.zip></span>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></div></body></html>