Posted by
AAM71 on
Aug 13, 2015; 7:26am
URL: http://imagej.273.s1.nabble.com/Bioformats-update-creates-exceptions-for-dm4-files-tp5014008.html
Dear Listers,
We are using Fiji quite a lot in our Facility. Until recently it was
able to read dm4 files from Gatan (even if this option is not mentioned
in documentation). However, after the update it became impossible -
instead of opening dm4 file Fiji produces the list of exceptions:
begin-----------------
(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.8.0_51 [64-bit]; Windows
7 6.1; 35MB of 6103MB (<1%)
java.lang.NumberFormatException: For input string: "0 . 0"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:506)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
at loci.formats.in.GatanReader.parseTags(GatanReader.java:468)
at loci.formats.in.GatanReader.initFile(GatanReader.java:197)
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:137)
at loci.plugins.in.Importer.run(Importer.java:75)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:212)
at ij.IJ.runPlugIn(IJ.java:176)
at ij.IJ.runPlugIn(IJ.java:165)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:212)
at ij.IJ.runPlugIn(IJ.java:176)
at ij.IJ.runPlugIn(IJ.java:165)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
at ij.io.Opener.openImage(Opener.java:360)
at ij.io.Opener.openImage(Opener.java:239)
at ij.io.Opener.open(Opener.java:106)
at ij.io.Opener.openAndAddToRecent(Opener.java:288)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:745)
end--------------------
I have tried to trace what is the reason and it seems that it is the
updated version of BioFormats plugin.
All versions before 5.1.0-m4 were fine to be able to read dm4 files (if
you install Bioformats plugin to ImageJ). Any version from 5.1.0-m4
upwards (newest is 5.1.3, I believe) produces the list of exceptions and
do not open dm4 files anymore.
I have uploaded the test image I have been using to
http://qa.openmicroscopy.org.uk/qa/upload/The name of the file is:
T2DM_3VBSED_roi_01_slice_0001.dm4
Can you, please, correct this bug? Or if it is impossible can you,
please, tell me how to install old Bioformats version to Fiji manually.
With ImageJ it is easy, but Fiji seems to have more complicated system.
I have sent thsi bug report to Bioformats list as well.
Sincerely,
Alex
--
Dr. Aleksandr Mironov MD, PhD
Senior Experimental Officer
D.1527, M.Smith Building
EM Core Facility, Faculty of Life Sciences
University of Manchester
Oxford Road
Manchester
M13 9PT
UK
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