Hello,
We are having difficulty opening datasets from our Lightsheet Z1 (.czi files, Zeiss) system in Fiji. Essentially we prefer to use Fiji for our reconstruction of multiview images. In order to do so, we need the original .czi file from the microscope to be subsetted to an individual .tif stack for each timepoint and angle (view). The ZEN software has the option to subset the data during acquisition into individual views and channels, unfortunately these files do not seem to be able to open in Fiji. Here is a quick summary, I am happy to upload sample data if you would like.
File structure:
Standard ZEN output: filename.czi
ZEN output for 2 colour image subsetted by channel: filename.czi; filename(1).czi
ZEN output for 2 channel, two angle (view) subsetted by channel and view: filename.czi; filename(1).czi; filename(2).czi; filename(3).czi
When opened in ZEN, the filename.czi file acts as a master index for all the others.
What can be opened:
A simple one channel, one angle(view) file can open in Fiji; however, if a second colour channel is added, the following error message appears:
(Fiji Is Just) ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 23MB of 14000MB (<1%)
java.lang.NumberFormatException: empty String
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:992)
at java.lang.Double.valueOf(Double.java:475)
at java.lang.Double.<init>(Double.java:567)
at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:1970)
at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1056)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:580)
at loci.formats.FormatReader.setId(FormatReader.java:1315)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
at ij.io.Opener.openImage(Opener.java:311)
at ij.io.Opener.openImage(Opener.java:334)
at ij.io.Opener.open(Opener.java:144)
at ij.io.Opener.openAndAddToRecent(Opener.java:247)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:662)
For a multi-channel (2-green,red) and multi-angle(view) (3) file that was separated by channel and view during acquisition (6 output files total) here is what happens:
Open the filename.czi file:
Appears to correctly open each angle(view) as a separate series with both colour channels in a hyperstack. (provided you have enough RAM or open as a virtual stack)
Open the filename(#).czi file
Either opens a hyperstack in which one colour channel contains no data, or opens two stacks, one of which is empty.
For a multi-channel (2), multi-angle(view) (3), and multi-timepoint (3) file that was separated by channel and angle(view) during acquisition (6 files total, each containing 3 timepoints) here is what happens:
Open the filename.czi file:
Does not open. left for >12 hours, no error messages. Fiji "Thread Killer" states "DrawAndDrop" function is still running.
Open the filename(#).czi file:
Does not open. left for >12 hours, no error messages. Fiji "Thread Killer" states "DrawAndDrop" function is still running.
In addition, Lightsheet files split using the File>New File Browser in ZEN Black can also not be opened. The same error message as above is outputted.
I am using Bio-Formats revision 4876596, May 12th build
Thanks for any help you can provide! If you would like the data sets, I'm happy to upload them.
-Doug
