fiji imagej crashes on Ubuntu 16.04

Question

I installed fiji (a distribution of imagej) on my Ubuntu 16.04 machine, and double-clicking the desktop icon opened the app for a second, or rather it tried to open, and then died. I looked for an answer online, and found on this page http://imagej.1557.x6.nabble.com/Fiji-crashes-UI-on-Ubuntu-all-recent-versions-td5005603.html that one can try

./ImageJ-linux64 --dry-run 

This prints out the run command used by the program. It calls the system java. So I copied out the command, and switched to use the included java (fiji and imagej come with their own java) and that fixed it. I have created a shell script with the command (referencing the included java executable), and this script works to start fiji.

Answer 1

Go to your fiji installation folder (Fiji.app or whatever it is called) and run

./ImageJ-linux64 --dry-run

This will output a long string, something like

java -Dpython.cachedir.skip=true -Dplugins.dir=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app -Xmx3714m -Xincgc -XX:PermSize=128m -Djava.class.path=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app/jars/imagej-launcher-4.0.5.jar -Dimagej.dir=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app -Dij.dir=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app -Dfiji.dir=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app -Dfiji.defaultLibPath=lib/amd64/server/libjvm.so -Dfiji.executable=./ImageJ-linux64 -Dij.executable=./ImageJ-linux64 -Djava.library.path=/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app/lib/linux64:/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app/mm/linux64 net.imagej.launcher.ClassLauncher -ijjarpath jars -ijjarpath plugins net.imagej.Main

Copy the command into a script file and substitute for the first 'java' the full path to the included java executable, something like

/home/pwarner/Schreibtisch/Bildanalyse/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/bin/java

Save the file in the directory (or wherever you like) and call it to start fiji, something like

./start_fiji.sh