[ImageJ-bugs] [Bug 950] New: Bioformats Plugin, problem opening .czi files
bugzilla at fiji.sc
bugzilla at fiji.sc
Fri Oct 31 07:39:04 CDT 2014
http://fiji.sc/bugzilla/show_bug.cgi?id=950
Bug ID: 950
Summary: Bioformats Plugin, problem opening .czi files
Product: Fiji
Version: unspecified
Hardware: PC
OS: Windows
Status: NEW
Severity: normal
Priority: P4
Component: Plugins
Assignee: imagej-bugs at imagej.net
Reporter: schmied at mpi-cbg.de
CC: schmied at mpi-cbg.de
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: It recognizes the illumination sides as channels.
3. Problem: Both wrong guesses 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 will provide an example dataset and share the link to my idisk via Email.
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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