--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jython_script.py	Tue Aug 04 13:21:32 2015 -0400
@@ -0,0 +1,34 @@
+import jython_utils
+import sys
+from ij import IJ
+from ij import ImagePlus
+
+VALID_IMAGE_TYPES = [ ImagePlus.GRAY8 ]
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+error_log = sys.argv[ -4 ]
+input = sys.argv[ -3 ]
+tmp_output_path = sys.argv[ -2 ]
+output_datatype = sys.argv[ -1 ]
+
+# Open the input image file.
+input_image_plus = IJ.openImage( input )
+bit_depth = input_image_plus.getBitDepth()
+image_type = input_image_plus.getType()
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.createImagePlus()
+image_processor_copy = input_image_plus.getProcessor().duplicate()
+input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
+
+try:
+    if image_type not in VALID_IMAGE_TYPES:
+        # Convert the image to binary grayscale.
+        IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
+    # Run the command.
+    IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" )
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
+except Exception, e:
+    jython_utils.handle_error( error_log, str( e ) )