In order to get CLIJ accessible from MicroManager 2.0 gamma scripting interface, please copy these files from the recent CLIJ release into the /plugins/ directory of MicroManager:
- clij_1.4.5.jar
- clij-clearcl-0.10.4.jar
- clij-core-1.4.5.jar
- clij-coremem-0.6.0.jar
- imagej-common-0.28.2.jar
- imglib2-realtransform-2.1.0.jar
- imglib2-ij-2.0.0-beta-44.jar
- clij-advanced-filters_-0.21.3.jar
- fiji-lib-2.1.2.jar
While copying these files, please make sure to remove older verrsions of the same dependencies, such as clij-clearcl-0.10.1.jar, imagej-common-0.26.1.jar and imglib2-realtransform-2.0.0.jar.
Afterwards, restart MicroManager. You can try if it works by running this beanshell script to see if it works.