Running imagej fails with the following message: Open other images in this ImageJ panel as follows: imagej -p 3 <image1> [<image2> ... <imageN>]
No JVM found to run ImageJ Please apt-get install a JVM to run ImageJ or set JAVA_HOME if it's not a JVM from a Debian Package. even though multiple JVM's are installed here. Bug #1556997 reported by Václav Šmilauer on 2016-03-14 Pleas, **FIX**this bug in the current LTS release (16.04) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Solution: The problem is that the /usr/bin/imagej script detects JAVA_HOME using JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | tail -1 | cut -d' ' -f 3) which is empty as the output of update-java-alternatives -l is (note multiple spaces between columns): java-1.6.0-openjdk-amd64 1061 /usr/lib/jvm/java-1.6.0-openjdk-amd64 java-1.7.0-openjdk-amd64 1071 /usr/lib/jvm/java-1.7.0-openjdk-amd64 java-1.8.0-openjdk-amd64 1081 /usr/lib/jvm/java-1.8.0-openjdk-amd64 and cut -d' ' -f3 selects space. The solution is to squeeze multiple spaces before running cut, so the line should read: JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | grep openjdk | sort | tail -1 | tr -s ' ' | cut -d' ' -f 3) which then gives the correct output (/usr/lib/jvm/java-1.8.0-openjdk-amd64 in my case) and makes imagej run as expected.
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