[BUG] ImageJ1 Macro - Analyze particles

ERROR ImageJ Macro         2:17       Error in row cropped.jpg: -1
ERROR ImageJ Macro         2:17       Execute failed: java.lang.ArrayIndexOutOfBoundsException: -1


This is the error it keeps throwing. The node before this node is also a Macro Node, performing watershed.

java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=nl_NL
Command-line arguments:  -os win32 -ws win32 -arch x86_64

Fri Nov 27 13:16:56 CET 2015
Unable to execute early startup code for an extension

java.lang.IllegalStateException: The profile is currently in use.
    at org.eclipse.equinox.internal.p2.engine.SimpleProfileRegistry.internalGetProfileStateProperties(SimpleProfileRegistry.java:1182)
    at org.eclipse.equinox.internal.p2.engine.SimpleProfileRegistry.getProfileStateProperties(SimpleProfileRegistry.java:1172)
    at org.eclipse.equinox.internal.p2.ui.sdk.scheduler.migration.MigrationSupport.isFirstTimeRunningThisSharedInstance(MigrationSupport.java:133)
    at org.eclipse.equinox.internal.p2.ui.sdk.scheduler.migration.MigrationSupport.performMigration(MigrationSupport.java:54)
    at org.eclipse.equinox.internal.p2.ui.sdk.scheduler.AutomaticUpdateScheduler.earlyStartup(AutomaticUpdateScheduler.java:90)
    at org.eclipse.ui.internal.EarlyStartupRunnable.runEarlyStartup(EarlyStartupRunnable.java:90)
    at org.eclipse.ui.internal.EarlyStartupRunnable.run(EarlyStartupRunnable.java:68)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.Workbench$56.run(Workbench.java:2812)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)


I was able to reproduce it. I copied this part of code from my FIJI macro into the marco node, then it occured again:


run("Set Measurements...", "area bounding shape display redirect=None decimal=3");


That was what I added, as the analyze particles standard macro just contains the area. I need the other values as well. Is there a different way to get them? Bounding rectangle, shape descriptor.

Hi Luuklag,

Thanks for reporting the bug. We will take care of it!

A more KNIMEish way to do it:

Binary Images -> Connected Component Analysis (append result in settings) -> Image Segment Features or Feature Calculator (BETA).

See also our example workflows on the Example Server (you can connect to it from KNIME itself).

Hope this helps,


Thanks, CCA works for me. Is there a way to rename the components after filtering?

Labeling Editor maybe?