<div dir="ltr"><div><div><div><div>Hi Martin,<br><br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">
PS - I hope this ist he right list to post. If not, maybe someone could direct me to the best suited forum<br></blockquote><br></div>This is definitely a problem in SCIFIO, so this was the right place to post! I've opened <a href="https://github.com/scifio/scifio/issues/123">a new issue</a> to track this problem and will look into it today.<br>
<br></div>Because this looks to be a bug in Bio-Formats as well (which is not surprising - as the SCIFIO TIFF support is derived from Bio-Formats) I am also forwarding this to the OME-Users list.<br><br></div>Thanks for the report!<br>
<br></div>- Mark<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jan 15, 2014 at 6:36 AM, Martin Höhne <span dir="ltr"><<a href="mailto:martin.hoehne@uk-koeln.de" target="_blank">martin.hoehne@uk-koeln.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear list,<br>
<br>
We have 16 bit Tiff files from a camera (from a Chemoluminescence detector. Fusion XL machine form Vilber Lourmat <a href="http://www.vilber.com/" target="_blank">http://www.vilber.com/</a>). The images can be opened fine in Fiji (open or drag&drop). However, importing via File>Import>BioFormats fails. I get this error:<br>
<br>
"Sorry, there was a problem during import". The log file is posted at the end of this mail.<br>
<br>
We are fine with the normal opening, however the ImageJ2 seems to try to open with the import function (2.0.0.0 beta7.6). I get this message:<br>
"io.scif.img.ImgIOExceprion: java.io.EOFException: Attempting to read beyond end of file"<br>
<br>
The image contains some metadata I can´t read when opening with ImageJ, but only when opening the file with the Fusion software from Vilber.<br>
For the attached file the metadata is at the end of this posting as well.<br>
<br>
The metadata is not so important, but it would be great if the images could be opened with ImageJ2 as well.<br>
<br>
Thank you<br>
Martin<br>
<br>
PS - I hope this ist he right list to post. If not, maybe someone could direct me to the best suited forum<br>
<br>
System information:<br>
Win7 64bit<br>
Fiji, updatet 2014-01-15<br>
<br>
Log from import:<br>
Fiji(legacy mode) File>Import>BioFormats:<br>
loci.formats.FormatException: loci.common.ReflectException: java.lang.reflect.InvocationTargetException<br>
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:202)<br>
at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:162)<br>
at loci.formats.FormatReader.setId(FormatReader.java:1360)<br>
at loci.formats.DelegateReader.setId(DelegateReader.java:275)<br>
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br>
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
at loci.plugins.in.Importer.run(Importer.java:79)<br>
at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
at ij.IJ.runUserPlugIn(IJ.java:196)<br>
at ij.IJ.runPlugIn(IJ.java:160)<br>
at ij.Executer.runCommand(Executer.java:131)<br>
at ij.Executer.run(Executer.java:64)<br>
at java.lang.Thread.run(Thread.java:662)<br>
Caused by: loci.common.ReflectException: java.lang.reflect.InvocationTargetException<br>
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:125)<br>
at loci.formats.in.TiffJAIReader.openBufferedImage(TiffJAIReader.java:197)<br>
... 13 more<br>
Caused by: java.lang.reflect.InvocationTargetException<br>
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br>
at java.lang.reflect.Method.invoke(Method.java:597)<br>
at ome.scifio.common.ReflectedUniverse.exec(ReflectedUniverse.java:317)<br>
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:122)<br>
... 14 more<br>
Caused by: java.io.EOFException<br>
at com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:329)<br>
at com.sun.media.jai.codec.SeekableStream.readFully(SeekableStream.java:306)<br>
at com.sun.media.jai.codec.SeekableStream.readUnsignedIntLE(SeekableStream.java:708)<br>
at com.sun.media.jai.codec.TIFFDirectory.readUnsignedInt(TIFFDirectory.java:524)<br>
at com.sun.media.jai.codec.TIFFDirectory.initialize(TIFFDirectory.java:289)<br>
at com.sun.media.jai.codec.TIFFDirectory.<init>(TIFFDirectory.java:125)<br>
at com.sun.media.jai.codecimpl.TIFFImage.<init>(TIFFImage.java:318)<br>
at com.sun.media.jai.codecimpl.TIFFImageDecoder.decodeAsRenderedImage(TIFFImageDecoder.java:112)<br>
... 20 more<br>
<br>
<br>
Metadata of attached image:<br>
Good Laboratory Practice:GLP<br>
<br>
GENERAL INFORMATION<br>
Title:<br>
Comments:<br>
Date: Freitag, 13. Dezember 2013<br>
Time: 13:42:04<br>
Image name: C:\Users\nephrolab\Pictures\temp_western\mhoehne\eva24__1.TIF<br>
<br>
Software information: FusionCapt Advance Solo 4 16.07<br>
<br>
ACQUISITION PARAMETERS:<br>
<br>
Lens information:<br>
Iris aperture:<br>
<br>
Camera information:<br>
Integration time acquisition: : 0 min 50 sec 0 msec<br>
Acquisition mode: Serial/r/n Image 1/10<br>
Positive acquisition<br>
Resolution used: Binning 2x2<br>
Pixel depth 16 Bit per pixel<br>
Software acquisition mode: Not defined<br>
Vigneting filter : Aperture value 0.84<br>
Sensor area used: : (0, 0, 2048,2048)<br>
Configuration file used: C:\Users\nephrolab\Documents\Vilber Lourmat\nephrolab_settings\2x2 binning.prt<br>
Camera serial number: 275704<br>
Tray position: Non applicable<br>
Application name: 2x2 binning<br>
Auto mode: User defined autoexposure coef 97%<br>
USB status: No USB detected<br>
Imaging system: FusionCapt Advance Solo 4 16.07<br>
Camera serial number: 275704 - Firmware >2.0.0<<br>
USB codage: No darkroom<br>
Lens configuration: Non applicable<br>
RGB status: Not installed<br>
Skylight: Not installed<br>
<br>
Image manipulation<br>
<br>
Gray level inversion: No<br>
<br>
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<br></blockquote></div><br></div>