[ome-users] Bio-Formats Importer .czi problem

[Emil Rozbicki]

Hi Christopher,

it seems like you have similar problems to those described here:
http://trac.openmicroscopy.org.uk/ome/ticket/12556

we have already have the fixes, they need to be tested now:
https://github.com/openmicroscopy/bioformats/pull/1386
https://github.com/openmicroscopy/bioformats/pull/1400

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.

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.

Regards,
Emil

On 31 Oct 2014, at 15:11, Christopher Schmied <schmied at mpi-cbg.de> wrote:

> 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: http://update.imagej.net/ (last check:20141026020028)
> Fiji: http://fiji.sc/update/ (last check:20141023165357)
> BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20140930145441)
> Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20141031022635)
> 
> Files not up-to-date:
>   c64b4276 (MODIFIED) 20141031124410 jars/ij-1.49j.jar
>   a2d4d92b (LOCAL_ONLY) 20140809134357 plugins/Read_Spim.jar
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> ome-users at lists.openmicroscopy.org.uk
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