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

Emil Rozbicki emil at glencoesoftware.com
Fri Nov 7 12:59:00 GMT 2014 

Hi Christopher,

Thanks for uploading the .CZI files to our server. I have checked the files and everything looks fine. 

Series count = 1
Series #0 :
	Image count = 620
	RGB = false (1) 
	Interleaved = false
	Indexed = true (false color, 16-bit LUT: 3 x 65536)
	Width = 1920
	Height = 1920
	SizeZ = 155
	SizeT = 1
	SizeC = 4 (2 Channel x 2 Illumination)

One thing to remember when working with .CZI is to always point the Bio-formatas importer at the master file (the one with no index). The indexed files may not give you the expected result. They will open but as you've noticed the metadata may be wrong.

There are two ways to open a stack, time point or series without reading the whole .CZI dataset. From the GUI using Plugins (menu)->Bio-Formats->Bio-Formats Importer choose .CZI master file. You’ll be prompted with Import options, in the “Memory management” select “Specify range for each series”, which will give you an option to specify a subset of data.
The other way is to use ImageJ macro, where you can also specify a subset of data to open, e.g.:

file="Some_File.czi";

run("Bio-Formats Importer", "open="+file+" color_mode=Default display_metadata display_ome-xml specify_range view=Hyperstack stack_order=XYCZT series_1 c_begin_1=1 c_end_1=1 c_step_1=1 z_begin_1=1 z_end_1=1 z_step_1=1");

run("Bio-Formats Importer", "open="+file+" color_mode=Default display_metadata display_ome-xml specify_range view=Hyperstack stack_order=XYCZT series_2 c_begin_2=1 c_end_2=1 c_step_2=1 z_begin_2=1 z_end_2=1 z_step_2=1");

I hope that helps. 

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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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