Release of Bio-Formats 5.3.3

bio-formats
Tags: #<Tag:0x00007fb876cc9288>

#1

Dear All,

Bio-Formats 5.3.3 is now available for Fiji from the Java 8 update site. If you have previously been using the Bio-Formats 5 update site, you will need to disable that as well as enabling the Java 8 site. This release includes:

Bug fixes for:

  • ImageJ - fix for issue when exporting from an ImagePlus ImageJ type that represents signed data. The pixel type will now remain unchanged as will the pixel values which had previously been scaled incorrectly
  • Tiff writing - using TiffWriter to write tiled images now supports the writing of BigTIFF datasets

File format fixes for:

  • Applied Precision CellWorX
  • NIFTI
  • Leica LIF (with thanks to Michael Goelzer)
  • Improvision TIFF
  • Metamorph

And more - see
https://www.openmicroscopy.org/site/support/bio-formats5.3/about/whats-new.html
for full details

The software is also available to download from
http://downloads.openmicroscopy.org/bio-formats/5.3.3

Any problems or comments, please use the OME Forums or mailing lists:

Regards,

The OME Team


#2

The newest release seems to have broken the Bio-Formats Exporter in Fiji

run("Mitosis (26MB, 5D stack)");
run("Bio-Formats Exporter", "save=[C:\\temp\\test.ics]");

Running this macro leads to the following exception:

(Fiji Is Just) ImageJ 2.0.0-rc-56/1.51h; Java 1.8.0_112 [64-bit]; Windows 7 6.1; 331MB of 96000MB (<1%)
 
java.lang.NullPointerException
	at loci.plugins.out.Exporter.run(Exporter.java:443)
	at loci.plugins.LociExporter.run(LociExporter.java:75)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:219)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:63)
	at ij.IJ.run(IJ.java:297)
	at ij.macro.Functions.doRun(Functions.java:601)
	at ij.macro.Functions.doFunction(Functions.java:96)
	at ij.macro.Interpreter.doStatement(Interpreter.java:230)
	at ij.macro.Interpreter.doStatements(Interpreter.java:218)
	at ij.macro.Interpreter.run(Interpreter.java:115)
	at ij.macro.Interpreter.run(Interpreter.java:85)
	at ij.macro.Interpreter.run(Interpreter.java:96)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
	at ij.IJ.runMacro(IJ.java:134)
	at ij.IJ.runMacro(IJ.java:123)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1039)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1035)
	at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:986)
	at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1035)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:97)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:144)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

I reported the issue on github as well.

Note: Version 5.3.2 doesn’t have this issue.


#3

Just as update following on from the Github issue, a fix for the Exporter bug mentioned above has been put in place. This will be included in the release of Bio-Formats 5.3.4 which is expected next week.