<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Christopher,<div><br></div><div>it seems like you have similar problems to those described here:</div><div><a href="http://trac.openmicroscopy.org.uk/ome/ticket/12556">http://trac.openmicroscopy.org.uk/ome/ticket/12556</a></div><div><br></div><div><div apple-content-edited="true">
<div><div><font face="Lucida Grande">we have already have the fixes, they need to be tested now:</font></div></div><div><a href="https://github.com/openmicroscopy/bioformats/pull/1386">https://github.com/openmicroscopy/bioformats/pull/1386</a></div><div><a href="https://github.com/openmicroscopy/bioformats/pull/1400">https://github.com/openmicroscopy/bioformats/pull/1400</a></div><div><br></div><div>To answer your question regarding the structure of the .CZI file format, currently Bioformats does not support reading a single .czi file from a dataset. The only way to open it correctly and access a subset of the dataset is as you described via Bioformats Importer choosing the Range option in the memory settings.</div><div><br></div><div>It would be great if we could get the data to check whether current fixes also solve your problems. As the files are larger then 2 GB they cannot be uploaded via the OME QA system. Would you mind uploading them to our FTP server, please. I will send you the details in a private e-mail.</div><div><br></div><div>Regards,</div><div>Emil</div>
</div>
<br><div><div>On 31 Oct 2014, at 15:11, Christopher Schmied <<a href="mailto:schmied@mpi-cbg.de">schmied@mpi-cbg.de</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div bgcolor="#FFFFFF" text="#000000">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<pre class="bz_comment_text" id="comment_text_0">Hello,
I have a .czi dataset which is a 2 channel 2 illumination side single view timeseries.
The 2 illumination sides are not fused. Each dimension is saved as an individual .czi file.
Thus there are 4 files per time point with the follwing order when they are saved by the microscope:
Time point 1; Channel 1; Right Illumination >> no index
Time point 1; Channel 2; Right Illumination >> index 1
Time point 1; Channel 1; Left Illumination >> index 2
Time point 1; Channel 2; Left Illumination >> index 3
Time point 2; Channel 1; Right Illumination >> index 4
etc...
For opening these files by dragging them into Fiji or selecting them via Bio-Formats Importer I use the following settings:
Hyperstack; Open Files Individually; Color mode: Default; Autoscale; Specify range for each series.
This opens the Bio-formats Range option.
The range for the z slices are correct. In this dataset 155 slices. But the Channels are incorrect.
For the first file of the dataset without index: C Begin = 1; C End = 4; 620 planes (4C x 155Z)
Interestingly if I give this file an index (such as 0) the behaviour is different then it does not recoginze any channels.
The next file with index 1: C Begin = 1; C End = 2; 310 planes (2C x 155Z)
Index 2: C Begin = 1; C End = 2; 310 planes (2C x 155Z)
Index 3: C Begin = 1; C End = 4; 620 planes (4C x 155Z)
Index 4 (first file of new timepoint): no channels recognized.
This pattern is repeated within each following time point.
1. Problem: It does not open the selected file as individual file.
It expects multiple channels and tries to open them thus I need to set the range.
2. Problem: The interpretations are not consistent within one time point.
At least the pattern is repeating so I was able to write a macro for now to circumvent this.
I can provide an example dataset with the above described 4 files (~2.8GB).
One question: the illumination sides seem to be recognized as channels.
I was made aware that this is the default interpretation of the importer for higher dimensions.
Is this correct?
Thanks a lot!
Christopher
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\Users\Public\DOCUME~1\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Users\Public\DOCUME~1\Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20141026020028)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20141023165357)
BigDataViewer: <a href="http://sites.imagej.net/Pietzsch/">http://sites.imagej.net/Pietzsch/</a> (last check:20140930145441)
Bio-Formats: <a href="http://sites.imagej.net/Bio-Formats/">http://sites.imagej.net/Bio-Formats/</a> (last check:20141031022635)
Files not up-to-date:
c64b4276 (MODIFIED) 20141031124410 jars/ij-1.49j.jar
a2d4d92b (LOCAL_ONLY) 20140809134357 plugins/Read_Spim.jar</pre>
</div>
_______________________________________________<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>