Error when running ScientiFig

Tags: #<Tag:0x00007fd542fa6d50> #<Tag:0x00007fd542fa6b98> #<Tag:0x00007fd542fa6a30>


Trying to run ScientiFig this evening, and immediately after selecting it from the Plugins menu, I get the following in an “Exception” text window.

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51q26; Java 1.8.0_144 [32-bit]; Windows 7 6.1; 19MB of 1024MB (1%)
java.lang.NoClassDefFoundError: org/apache/batik/ext/awt/image/spi/RegistryEntry
	at ij.IJ.runUserPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(
Caused by: java.lang.ClassNotFoundException: org.apache.batik.ext.awt.image.spi.RegistryEntry
	at java.lang.ClassLoader.loadClass(
	at sun.misc.Launcher$AppClassLoader.loadClass(
	at java.lang.ClassLoader.loadClass(
	... 6 more

I’ve uninstalled and reinstalled via the Fiji updater. I’m not the expert on Java errors, but it looks like maybe Batik is a dependency, and is no longer installed? Would manually installing an earlier version of ScientiFig pull it back in, or is Batik installed via some other package? Or am I off in the weeds?


OK, slightly embarrassed to be posting a fix this quickly. My search for ScientiFig came up dry, but searching for Batik resulted in this post, explaining that it is related to the Java 6 Legacy/Java 8 update sites that have been mentioned a couple times. In my case, I need to enable the Java 8 update site.



Dear Jim,

there are two ways to solve the issue:

1- If you don’t mind updating your FIJI then download and install the latest FIJI (bundled with java 8) from ‘’. Launch this new FIJI and run the updater to install the ‘ScientiFig’ update site (please see for a great tutorial on update sites)

2- If, on the other hand, you prefer to keep your ‘aging’ FIJI as it is (and/or prefer to keep using java 1.6), then you must enable the new ‘Scientifig-deprecated’ update site together with the ‘Fiji-Legacy’ update site while inactivating the ‘ScientiFig’ and the ‘java-8’ update sites.

Both solutions should work, but please let me know otherwise. Please also note that ‘Scientifig-deprecated’ is an old version of the software that contains a few known bugs and that will never be updated. I just created it for users that have an old FIJI bundled with java 6 and prefer not to install a more recent version (probably because they fear they may lose cool plugins during the transition, which is something I can totally understand).

For the record the issue comes from the fact that ‘FIJI-legacy’ contains batik 1.8 whereas ‘java-8’ contains batik 1.9 and some classes have been moved between the two versions of the batik library making it hard/impossible to use the same code with both versions (and thereby making the last version of SF not compatible with old FIJIs). Hopefully, I’ll be able to find a better fix for that in the future rather than creating a deprecated update site, but that is the only solution that came to my mind for now.

Sorry for the inconvenience and thanks a lot for using this software.



ps: I have just modified the SF launcher so that it reports all problems it can detect and prints several guidelines on how to fix these issues