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Bug 950 - Bioformats Plugin, problem opening .czi files
Bioformats Plugin, problem opening .czi files
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-10-31 07:39 CDT by Christopher Schmied
Modified: 2016-04-22 16:36 CDT
3 users (show)

See Also:

Description Christopher Schmied 2014-10-31 07:39:04 CDT
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
Comment 1 Mark Hiner 2014-10-31 08:25:31 CDT
Hi Christopher,

 Thank you for taking the time to report this issue. The Bio-Formats importer is managed by the OME team; they have a separate system for issue tracking and resolution. See: http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html for instructions on reporting bugs.

 As a side note, I would point out that Bio-Formats uses a fixed 5-dimensional (XYZCT) data model, employing a modulo system for representing higher dimensions (e.g. ideally it would use modulo along C to track illumination in your dataset). But my understanding is that you would not see a dedicated "Illumination" axis using Bio-Formats right now.

 SCIFIO does can do arbitrary axes for N-D data, but would use Bio-Formats anyway for CZI support.

 But it does still sound like 1) and 3) are bugs that should be reported.
Comment 2 Christopher Schmied 2014-10-31 10:15:02 CDT
Hi Mark,

Thank you for your response. 
I submitted my report to the OME mailing list.

Thanks for the info about the data model. This might be indeed the case.
I modified my report accordingly.
Comment 3 Curtis Rueden 2016-04-22 16:36:07 CDT
Reported to the OME team, as reported by Christopher Schmied.