[ome-users] Bioromats update creates exceptions for dm4 files

[Aleksandr Mironov]

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 the 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 and 
above (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.


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

E-mail: Aleksandr.Mironov at manchester.ac.uk
http://www.ls.manchester.ac.uk/research/facilities/