Error when using FindFoci plugin

Hi everyone,

I try to use FindFoci plugin.

I use it through a macro with this command:

run("FindFoci", "mask=(None) background_method=[Auto threshold] background_parameter=3.0 auto_threshold=Default statistics_mode=Both search_method=[Half peak value] search_parameter=0.5 minimum_size=100 minimum_above_saddle connected_above_saddle minimum_peak_height=[Absolute height] peak_parameter=1.0 sort_method=[Average intensity] maximum_peaks=1 show_mask=[Fraction height above background] fraction_parameter=0.3 show_table clear_table show_log_messages remove_edge_maxima object_analysis gaussian_blur=5.0 centre_method=[Centre of mass (search image)] centre_parameter=2.0");

I get this error :
(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51t; Java 1.8.0_144 [64-bit]; Windows 10 10.0; 47MB of 12000MB (<1%)

java.lang.NoClassDefFoundError: ij/gui/ExtendedGenericDialog
	at gdsc.foci.FindFoci.run(FindFoci.java:695)
	at ij.IJ.runUserPlugIn(IJ.java:221)
	at ij.IJ.runPlugIn(IJ.java:185)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at ij.IJ.run(IJ.java:301)
	at ij.macro.Functions.doRun(Functions.java:602)
	at ij.macro.Functions.doFunction(Functions.java:96)
	at ij.macro.Interpreter.doStatement(Interpreter.java:248)
	at ij.macro.Interpreter.doStatements(Interpreter.java:234)
	at ij.macro.Interpreter.run(Interpreter.java:117)
	at ij.macro.Interpreter.run(Interpreter.java:88)
	at ij.macro.Interpreter.run(Interpreter.java:99)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:161)
	at ij.IJ.runMacro(IJ.java:138)
	at ij.IJ.runMacro(IJ.java:127)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1096)
	at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:1092)
	at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:1043)
	at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:1092)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:137)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: ij.gui.ExtendedGenericDialog
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 30 more'

If I use this plugin with the FindFoci GUI with the same settings, it works.

Does anyone understand these errors to help me to solve my problem?

Thanks in advance,

Regards

Fabien

I’ve just tried with ImageJ 1.51 (not Fiji) and FindFoci used with the macro works. Does anyone have an idea?

Thanks

The developer of the plugin helped me. Below his answer by email:

The GDSC and GDSC-SMLM update sites both use the same gdsc-core jar library. However the GDSC-SMLM site has an older version. This site has not been updated since 2016-09. When you check both update sites in Fiji it seems that the older version wins over the newer version.
Basically you can only run the GDSC plugins or the GDSC-SMLM plugins, but not both together. This will be fixed in the future but for now you will have to remove the GDSC-SMLM update site.
The current version of the GDSC-SMLM plugins are not documented so haven’t been released. If you want to use the GDSC SMLM plugins then I can provide them to you. They will be able to run in parallel with the GDSC plugins.

I personnaly don’t need GDSC-SMLM. If a reader of this topic need it, send an email to the developer. Email address available on this page: http://www.sussex.ac.uk/gdsc/people/person/270682

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Hi Fabien,

The FindFoci plugin seems to ironically be very difficult to find. It’s no longer on the University of Sussex website. I was wondering if you would be willing to email it to me, or tell me where it is, if you know?

Many thanks,
Adam

For anyone reading this thread and looking for the FindFoci plugin, part of the GDSC plugin suite:

  • You can get the plugin by subscribing to one of the GDSC or the GDSC-SMLM update sites.

  • The publication describing the plugin is here:

  • The source code is available here:

It seems the author of the plugin and publication is also on this forum: @alexherbert

The Find Foci web page does still exist. It was relocated to a part of the intranet for the microscopy support pages of the department:

http://www.sussex.ac.uk/gdsc/intranet/microscopy/UserSupport/AnalysisProtocol/imagej

This page is hard to find when you know where it is. It wasn’t my idea to relocate it.

Note that if you type “GDSC find foci” into Google then this page is the top hit. So it is indexed by search engines.

As for the original problem of incompatibility between various GDSC plugins via the ImageJ update sites then the fix is to use one or the other but not both. A new vesion of the GDSC SMLM plugins coming soon will eliminate this and allow them to be installed side-by-side.

Alex

1 Like