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

[Christopher Schmied]

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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