I  have a problem running a macro that has been used for some time using ImageJ. Here is a small part that does not work as expected. 

macro"sum_dark"{

////////////////////////////////////////////////////////////Dark 
    Darkdir = getDirectory("Choose DarkField Directory ");
    Darklist = getFileList(Darkdir);
    setOption("display labels", true);
    Darkpath = Darkdir+Darklist[0];
    DarkOpenpath="open=["+Darkpath+"]";
    DarkFileCount=lengthOf(Darklist);    

run("Image Sequence...", "open = " + DarkOpenpath+" number="+DarkFileCount+" starting=1 increment=1 scale=100 file=[] or=[] sort");
rename("Raw Dark Fields");

run("Z Project...", "start=1 stop="+DarkFileCount+" projection=[Average Intensity]");
rename("Average Dark Field");

selectWindow("Raw Dark Fields");
close();

The macro fails to open tifs giving the messege: Open TIFF: ImageJ cannot open 12-bit LZW-compressed TIFFs

The exception is:

(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49i; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 36MB of 24000MB (<1%)
 
java.io.IOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid TIFF file
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:273)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
	at net.imagej.legacy.DefaultLegacyHooks.interceptOpenImage(DefaultLegacyHooks.java:336)
	at ij.plugin.FolderOpener.run(FolderOpener.java:115)
	at ij.IJ.runPlugIn(IJ.java:172)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at ij.IJ.run(IJ.java:272)
	at ij.macro.Functions.doRun(Functions.java:591)
	at ij.macro.Functions.doFunction(Functions.java:89)
	at ij.macro.Interpreter.doStatement(Interpreter.java:227)
	at ij.macro.Interpreter.doBlock(Interpreter.java:599)
	at ij.macro.Interpreter.runFirstMacro(Interpreter.java:698)
	at ij.macro.Interpreter.doStatement(Interpreter.java:260)
	at ij.macro.Interpreter.doStatements(Interpreter.java:215)
	at ij.macro.Interpreter.run(Interpreter.java:112)
	at ij.macro.Interpreter.run(Interpreter.java:82)
	at ij.macro.Interpreter.run(Interpreter.java:93)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
	at ij.IJ.runMacro(IJ.java:119)
	at ij.IJ.runMacro(IJ.java:108)
	at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:782)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:156)
	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$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)
Caused by: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid TIFF file
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:551)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
	... 36 more
Caused by: java.io.IOException: io.scif.FormatException: Invalid TIFF file
	at io.scif.AbstractReader.setSource(AbstractReader.java:274)
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
	... 38 more
Caused by: io.scif.FormatException: Invalid TIFF file
	at io.scif.formats.MinimalTIFFFormat$Parser.typedParse(MinimalTIFFFormat.java:412)
	at io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:867)
	at io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:849)
	at io.scif.AbstractParser.parse(AbstractParser.java:252)
	at io.scif.AbstractParser.parse(AbstractParser.java:335)
	at io.scif.AbstractParser.parse(AbstractParser.java:52)
	at io.scif.AbstractReader.setSource(AbstractReader.java:270)
	... 40 more


Note that using File -> Import -> image sequence does correctly open the images. Later in the script it opens the images one at a time to apply the corrections and this part works.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows NT (unknown)
  os.version => 6.2
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PORTAB~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\PORTAB~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141015111008)
Fiji: http://fiji.sc/update/ (last check:20141014035500)

Files not up-to-date:
  5996920b (LOCAL_ONLY) 20140806103157 plugins/BMIT/KES_barium.ijm
  7676da49 (LOCAL_ONLY) 20140719201650 plugins/BMIT/KES_iodine.ijm
  1bc4fefb (LOCAL_ONLY) 20141009122730 plugins/BMIT/Micro-CT-Processing_V2.2.ijm
  cd71f0a5 (LOCAL_ONLY) 20140319113354 plugins/BMIT/Vertical_Scan.ijm
  d3447486 (LOCAL_ONLY) 20140629143622 plugins/BMIT/normalize_one.ijm
  76b3e9ee (LOCAL_ONLY) 20141015154722 plugins/BMIT/sum_dark.ijm