Open Microscopy Environment

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

Hi,

We're currently testing a number of CZI fixes (https://github.com/openmicroscopy/bioformats/pull/1078). I'm not sure if these were included in the build of Bio-Formats you were testing with though. If you were using a 5.0 development build, you should have, otherwise probably not. We should be making a 5.0.2 release containing these fixes in the next week or so.

Either way, if you'd like to upload a sample image demonstrating the problems you described using https://www.openmicroscopy.org/qa2/qa/upload/ then we can take a look at it in more detail and check if our current fixes cover your case or if further work is needed to support them.


Many thanks,
Roger Leigh

Hi Roger,

The 5.0.2 release has helped with a few files, but not all. I'll upload some of the ones I'm still having difficulty with.

Thanks,

Doug

Unfortunately all of the files are over 2GB is there another method to get them to you?

Thanks,

Doug

Hi Doug,

Alternate upload instructions have been sent in a private message. If you have any trouble uploading with those instructions, please let us know.

Regards,
-Melissa