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

[Balaji Ramalingam (Staff)]

Hi Alex,

Thank you for submitting your file.
We were able to reproduce the issue locally,and a PR has been opened to
fix this issue:
https://github.com/openmicroscopy/bioformats/pull/1928

It will get merged post our reviewing process, and will most probably be
available in the next stable release of Bio-Formats (5.1.4).

Regarding the manual upgrade/downgrade of Bio-Formats in FIJI:
Please use the following link to do the same,
http://www.openmicroscopy.org/site/support/bio-formats5.1/users/fiji/#manua
l-upgrade

Hope that helps.

Best,
Balaji


__________________
Mr Balaji Ramalingam
Software Developer

OME Team
College of Life Sciences
University of Dundee






On 12/08/2015 11:18, "Aleksandr Mironov"
<Aleksandr.Mironov at manchester.ac.uk> wrote:

>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/
>_______________________________________________
>ome-users mailing list
>ome-users at lists.openmicroscopy.org.uk
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