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<p class="MsoNormal"><span lang="EN-US">Dear Bioformats team,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I have a problem with the Bioformats command line tool.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I want to extract individual z planes from Zeiss .czi files and according to the documentation the Bioformats command line tool bfconvert can be used for this. However, I can’t get this feature to work. I can convert
a whole file from .czi to .tif but I cannot extract individual planes apart from the first one. I use the following code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">bfconvert –z 1 “...\ZStack.czi” “...\converted.tiff”<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">and as an error message I get<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">“Plane index: 1 must be <1”<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(with –z 0 it works)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE"><img width="674" height="343" id="Picture_x0020_1" src="cid:image001.png@01CF6AAE.C4660DB0"></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Also if I try to use the patterns to save all z planes as individual files with the following code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">bfconvert –z 1 ...\ZStack.czi ...\converted%z.tiff<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">a file with the name convertedz.tiff is saved which contains all z planes.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If I look at the metadata the zSize is recognised correctly and also if I use showinf.bat or the ImageJ plugin the file is read and displayed correctly.
</span><span style="mso-fareast-language:DE"><img width="644" height="366" id="Picture_x0020_2" src="cid:image002.png@01CF6AAF.98FE7DF0"></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE"><img width="384" height="493" id="Picture_x0020_3" src="cid:image003.png@01CF6AAF.98FE7DF0"></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">With the ImageJ plugin I can then also export the z planes as individual files.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Ultimately, I want to do this conversion for large czi files (extracting time points, series and z planes) as part of a pipeline so I would prefer to use the command line tool not the ImageJ plugin.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am using Version 5.0.1 of Bioformats (VCS revision: b5a33f3, Build date: 3 April 2014),<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR">Java version 1.7.0_55 (Java (TM) SE Runtime Environment (Build 1.7.0._55-b13), Java Hotspot (TM) 64-Bit Server VM (Build 24.55-b03, mixed mode))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Windows 7 Professional Service Pack 1 (64-bit)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I have attached a small .tif file for which I get the same problem, but am happy to provide the original .czi file if you let me know how.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you need any further information, please let me know.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you and best wishes<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Sabine<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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