[ome-users] bioformats czi file reading

[Sebastien Besson (Staff)]

Hi Alejandro,

given the Java version indicated in your error message, I suspect you are using
Bio-Formats 5.1.10 or older since this the last version of Bio-Formats which
supports Java 6.

We had previous reports of this error which should has been fixed in more recent
versions of the Bio-formats plugin. To be able to use it, you will need to upgrade your
Fiji distribution to use the version bundled Java 8 and activate the Java-8 update site. [1]

Best,
Sebastien

[1] https://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D

On 25 Oct 2017, at 02:19, Alejandro Pedro Pariani <apariani846 at gmail.com<mailto:apariani846 at gmail.com>> wrote:


Hi,
can't get bioformats to open some czi files captured on a new Zeiss
LSM880.  I've tried to do so using Fiji and ImageJ
Example error message below:

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51r; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 25MB of 4509MB (<1%)
java.lang.NumberFormatException: null
              at java.lang.Integer.parseInt(Integer.java:417)
              at java.lang.Integer.parseInt(Integer.java:499)
              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:221)
              at ij.IJ.runPlugIn(IJ.java:185)
              at ij.IJ.runPlugIn(IJ.java:174)
              at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
              at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
              at ij.IJ.runUserPlugIn(IJ.java:221)
              at ij.IJ.runPlugIn(IJ.java:185)
              at ij.IJ.runPlugIn(IJ.java:174)
              at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:514)
              at ij.io.Opener.openImage(Opener.java:368)
              at ij.io.Opener.openImage(Opener.java:242)
              at ij.io.Opener.open(Opener.java:109)
              at ij.io.Opener.openAndAddToRecent(Opener.java:291)
              at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
              at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
              at java.lang.Thread.run(Thread.java:662)

Cheers,

Alexander Peter Pariani
PhD student
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