Hi, thanks for your reply. I think I’ve been using java 8 with java8 update sites enabled. To be sure I’ve tryed a downloading a fresh Fiji, as you suggested. Is it correct that this comes with java 8 bundled by default and java 8 update sites enabled? After downloading, I ran the updater which told me it is indeed up-to-date. In Plugins > Utilities > ImageJ Properties I find for java.version: 1.8.0_66, afaik this does correspond to Java.
Here is what I get in the console:
$ ImageJ-win64.exe --headless --console -macro test.ijm
$ Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
After which I have to ctrl-C to exit, which is of course only a slight inconvenience but I’m wondering if I’m doing something wrong. Also, I just noticed that after I run the command a new ‘line’ in the command line is opened (this smit@HPLAPTOP …). I’m not sure if this is related to the issue I’m having.
The script I’m trying to run:
Where I replace the last line with the other options,
Finally, is it possible that other installations of ImageJ are interfering with this instance? I sometimes get the error:
[ERROR] Could not connect to existing ImageJ instance. If problem persists, please delete file: C:\Users\Smit\AppData\Local\Temp\ImageJ-Smit-7.stub