This bug has been reported also in debian, as bug #820097. 
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820097)...
and fixed. The fixed version is already available for the next Ubuntu 
(Yakkety), in version 1.50i+dfsg-1. So maybe importing that newer version in 
Xenial would be fine.

Alternatively, the fix is a one line patch:
--- imagej-1.50d+dfsg/debian/imagej.sh  2014-03-12 12:58:36.000000000 +0000
+++ imagej-1.50i+dfsg/debian/imagej.sh  2016-04-07 12:57:41.000000000 +0000
@@ -29,7 +29,7 @@
 
 if [ -z "$JAVA_HOME" ] ; then
     # This does not work see #505315
-    JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | 
tail -1 | cut -d' ' -f 3)
+    JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | 
tail -1 | tr -s ' ' | cut -d' ' -f 3)
     # Reverted to old version - see #558222 (Andreas Tille)
     # JAVA_HOME=$(dirname $(dirname $(dirname $(readlink 
/etc/alternatives/java))))
     # Also suggested by From: JR Coding <jr.cod...@googlemail.com>; To: 
740...@bugs.debian.org


** Bug watch added: Debian Bug tracker #820097
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820097

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https://bugs.launchpad.net/bugs/1556997

Title:
  JAVA_HOME auto-detection fails due to whitespace in update-java-
  alternatives output

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