<div dir="ltr">Hi all,<br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 15, 2015 at 5:51 AM, William Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Ji,<div><br></div><div>I tried opening with an updated Fiji (Bio-formats 5.1.1 and I see the same as you.</div><div>It looks like this is actually a 16-bit image that only contains 8-bit data.</div><div>The Original Metadata has:</div><div>BitsPerPixel 8</div><div>PixelType uint16</div><div><br></div><div>Bio-formats is reading the BitsPerPixel incorrectly, since it's setting the "SignificantBits" attribute to 16 (see screenshot).</div><div>I've created a ticket to fix this bug: <a href="https://trac.openmicroscopy.org/ome/ticket/12885" target="_blank">https://trac.openmicroscopy.org/ome/ticket/12885</a></div><div><br></div><div><br></div><div>Downloading the bioformats package from <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.1/" target="_blank">http://downloads.openmicroscopy.org/bio-formats/5.1.1/</a> and running</div><div>java -jar bioformats_package.jar ZEN\ 2\ Blue\ 8bit.czi</div><div>Seemed to work fine for me.</div></div></blockquote>This is <a href="https://github.com/CellProfiler/python-bioformats/issues/25">issue 25</a> in python-bioformats. Now that I have the file, I'll test it myself against bioformats_package 5.1.1 and see if pointing the JVM at that jar fixes the problem. I'll report back with instructions for launching python-bioformats with the updated jar if it works. I guess this is a case of data in two places leading to an unfortunate misinterpretation (8 bits per pixel / data type 16 bit unsigned). It might make sense for me to check for this discrepancy and, although technically not my fault, the wise choice is to favor BitsPerPixel.<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div>The Show Metadata option gave me this (showing SizeC = 1 and SizeT = 1).</div><div><br></div><div><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"></div><div><br></div><div><br></div><div>Downloading the command line tools from the above url, and running</div><div><br></div><div>$ ./showinf ZEN\ 2\ Blue\ 8bit.czi</div><div><br></div><div>seemed to open the image fine. With…</div><div><br></div><div><div>Filename = /Users/wmoore/Documents/ZEN 2 Blue 8bit.czi</div><div>Series count = 1</div><div>Series #0 :</div><div><span style="white-space:pre-wrap"> </span>Image count = 1</div><div><span style="white-space:pre-wrap"> </span>RGB = false (1) </div><div><span style="white-space:pre-wrap"> </span>Interleaved = false</div><div><span style="white-space:pre-wrap"> </span>Indexed = true (false color)</div><div><span style="white-space:pre-wrap"> </span>Width = 256</div><div><span style="white-space:pre-wrap"> </span>Height = 256</div><div><span style="white-space:pre-wrap"> </span>SizeZ = 1</div><div><span style="white-space:pre-wrap"> </span>SizeT = 1</div><div><span style="white-space:pre-wrap"> </span>SizeC = 1</div><div><span style="white-space:pre-wrap"> </span>Thumbnail size = 128 x 128</div><div><span style="white-space:pre-wrap"> </span>Endianness = intel (little)</div><div><span style="white-space:pre-wrap"> </span>Dimension order = XYCZT (certain)</div><div><span style="white-space:pre-wrap"> </span>Pixel type = uint16</div><div><span style="white-space:pre-wrap"> </span>Valid bits per pixel = 8</div><div><span style="white-space:pre-wrap"> </span>Metadata complete = false</div><div><span style="white-space:pre-wrap"> </span>Thumbnail series = false</div><div><span style="white-space:pre-wrap"> </span>-----</div><div><span style="white-space:pre-wrap"> </span>Plane #0 <=> Z 0, C 0, T 0</div><div><br></div><div><br></div><div>Reading pixel data (0-0)</div><div><span style="white-space:pre-wrap"> </span>************ no LUT for plane #0 ************</div><div><span style="white-space:pre-wrap"> </span>Read 1/1 planes (100%)</div><div>[done]</div><div>0.121s elapsed (121.0ms per plane)</div><div><br></div><div>Launching image viewer</div></div><div>….</div><div><br></div><div><br></div><div>Are these the exact same jars that you downloaded?</div><div>I'm afraid I can't reproduce the problems you're having here and can only suggest you try again.</div><div><br></div><div> Hope you can get this working.</div><div>If it still fails to open, please send us any error messages or other info that might help to fix this.</div><div><br></div><div> Regards,</div><div><br></div><div> Will.</div><div><br></div><div><br></div><div><br></div><div><img height="796" width="957" src="cid:D033EA9C-F4A5-47BE-B88D-3CC1B31EB59B@lifesci.dundee.ac.uk"></div><div><br></div><div><br><div><div>On 15 May 2015, at 07:05, "Tang Ji" <<a href="mailto:tangji0318@foxmail.com" target="_blank">tangji0318@foxmail.com</a>> wrote:</div><br><blockquote type="cite"><div>Dear,</div><div>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.</div><div><span><3006CB03@F490172D.BD8C5555></span></div><div><br></div><div>Then I tried to open the .czi file with upgraded Fiji, but it fails completely.</div><div><span><2803D008@F490172D.BD8C5555></span></div><div><br></div><div>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.</div><div><span><290ACF05@F490172D.BD8C5555></span></div><div><br></div><div>Finally, if I use command "java -jar loci_tools.jar", I even cannot open the file.</div><div>I'll really appreciate you if you know how to solve the problem. Thanks.</div><div><br></div><div>Ji</div><div>May 15, 2015</div><span><290ACF05@F490172D.BD8C5555></span><span><2803D008@F490172D.BD8C5555></span><span><3006CB03@F490172D.BD8C5555></span><span><ZEN 2 Blue 8bit.czi></span>_______________________________________________<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></blockquote></div><br></div></div><br>_______________________________________________<br>
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