I use a macro in fiji to process my images from the confocal microscope. These images are typically zstack images with multiple colours, and I use the macro to condense the zstacks, and then save each colour componant as well as a merged RGB image.

The problem occurs when the macro tries to open a file whos name begins in any latter from J-Z, whereupon I get an error message saying "there are no images open" and the exception below[1]. If the file begins with a 1-9 or the letters a-i, it will be openned and processed fine. If I rename the file with an "a" in front, it will also be openned fine. For example the file "Untransfected" will not open, but renaming the exact same file to "aUntransfected" will open fine.

This only occurs with zstack images. If I try and open a non-zstack 3 colour image it also opens fine no matter what it is called.

I usualyl use .lif image files that open using the Bio-Formats plugin in fiji. However .lif files that are not z-stacks open fine, as well as zstacks renamed to begin with a letter between a-i, so it it is not the file type itself that is the problem.

I have pasted a sample macro that I use below [2]




[1]

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51a; Java 1.8.0_51 [64-bit]; Mac OS X 10.10.5; 394MB of 6164MB (6%)
 
loci.formats.UnknownFormatException: Unknown file format: /Users/philipdusart/Google Drive/PhilWorkShared/confocal/160509/160429/test/Icon
	at loci.formats.ImageReader.getReader(ImageReader.java:190)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:630)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:486)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:139)
	at loci.plugins.BF.openImagePlus(BF.java:92)
	at loci.plugins.macro.LociFunctions.openImagePlus(LociFunctions.java:216)
	at sun.reflect.GeneratedMethodAccessor27.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:82)
	at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)
	at ij.macro.Functions.doExt(Functions.java:4490)
	at ij.macro.Functions.getStringFunction(Functions.java:274)
	at ij.macro.Interpreter.getStringTerm(Interpreter.java:1293)
	at ij.macro.Interpreter.getString(Interpreter.java:1272)
	at ij.macro.Interpreter.doStatement(Interpreter.java:281)
	at ij.macro.Interpreter.doBlock(Interpreter.java:608)
	at ij.macro.Interpreter.runUserFunction(Interpreter.java:311)
	at ij.macro.Interpreter.doStatement(Interpreter.java:233)
	at ij.macro.Interpreter.doFor(Interpreter.java:530)
	at ij.macro.Interpreter.doStatement(Interpreter.java:254)
	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:133)
	at ij.IJ.runMacro(IJ.java:122)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:936)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:933)
	at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:899)
	at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:933)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:163)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
	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)



[2]

function action(input, output1, output2, output3, output4, filename) {
run("Bio-Formats Macro Extensions");
Ext.openImagePlus(input + filename)
run("Z Project...", "projection=[Max Intensity]");
          rename("A"); 
  run("Split Channels"); 
selectWindow("C3-A");
setMinAndMax(1, 75);
run("Apply LUT");
selectWindow("C2-A");
setMinAndMax(1, 72);
run("Apply LUT");
run("Merge Channels...", "c1=[C2-A] c2=[C3-A] c3=[C1-A] keep");
selectWindow("RGB");
saveAs("Tiff", output1 + filename);
close();
run("Merge Channels...", "c2=[C3-A] c3=[C1-A] keep");
selectWindow("RGB");
saveAs("Jpeg", output3 + filename);
selectWindow("C3-A");
saveAs("Jpeg", output2 + filename);
selectWindow("C2-A");
saveAs("Jpeg", output4 + filename);
close();
close();
close();
close();
close();
}
input = "/Users/philipdusart/Google Drive/PhilWorkShared/confocal/160509/160429/STATIC/";
output1 = "/Users/philipdusart/Google Drive/Other data/Confocal/1Processed/160509/160429/STATIC/RGB/";
output2 = "/Users/philipdusart/Google Drive/Other data/Confocal/1Processed/160509/160429/STATIC/green/";
output3 = "/Users/philipdusart/Google Drive/Other data/Confocal/1Processed/160509/160429/STATIC/G+B/";
output4 = "/Users/philipdusart/Google Drive/Other data/Confocal/1Processed/160509/160429/STATIC/red/";

list = getFileList(input);
for (i = 0; i < list.length; i++)
action(input, output1, output2, output3, output4, list[i]);
setBatchMode(false);

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.5
  java.version => 1.8.0_51
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_51-b16
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.51-b03
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160504203521)
Fiji: http://update.fiji.sc/ (last check:20160509100721)