[ome-users] multi-scene .czi files

[Oliver Brookes]

Hi Sebastien,


I've uploaded one of my problem files. How do I check the bioformats version number please? I have the update site checked in the FIJI options, and I keep FIJI up to date, so I expect it to be the right version.

The images don't open. It throws an error message very similar to the one reported by Michael Cammer on the OME list in march of this year. My error log contents are:


(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51a; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 41MB of 6009MB (<1%)

java.lang.NumberFormatException: null
at java.lang.Integer.parseInt(Integer.java:542)
at java.lang.Integer.parseInt(Integer.java:615)
at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2268)
at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1329)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:731)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)



Let me just clarify that this only happens on multi-position images. Normal images, stacks and videos open fine. When I hover the mouse over the files that won't open (in windows 7), or look at their properties, they all have XYCZTSB dimensions, but the ones that will open all only have XYCZT. If I use the zen software to split the images into individual scenes, the scenes still retain the XYCZTSB, although S and B now always have a value of 1, and they still fail to open and throw the error message.


Thanks for looking into this,


Oliver

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk>
Sent: 06 June 2016 11:02:00
To: users OME
Subject: Re: [ome-users] multi-scene .czi files

Hi Oliver,

the Zeiss scene dimension should be supported by Bio-Formats and we certainly have
several representative CZI datasets including multiple scenes tested daily.

Could you first of all confirm you are using Bio-Formats 5.1.10 in Fiji? Also, can you give us
more detail about the issue: is an error thrown by Bio-Formats when opening the file or is a
single position opened with wrong dimensions? Finally do you have a sample file that you could
upload to http://qa.openmicroscopy.org.uk/qa/upload/ to reproduce the issue?

Best,
Sebastien

On 2 Jun 2016, at 10:25, Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>> wrote:


Hello, I've found that it's not possible to open multiple scene Zeiss images using bioformats in FIJI. Using the "positions" option on our Zeiss Elyra, it's possible to store multiple locations and automatically take pictures (very good for timelapse video). The positional info is stored in the .czi format as a "scene" dimension - the dimensions of the file are listed as XYCZTSB. I can open czi images, stacks and movies that are taken at single positions (anything where the dimensions of the .czi file are XYCZT). Is the extended .czi format not supported?


Thanks,


Oliver

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