![]() ![]() You can close all image displays at the end of each cycle by placing a Run_ImageJ module that executes the "File > Close All" command after the last Run_ImageJ module in your pipeline. You may find that image displays accumulate as your pipeline runs (press the "Show" button on the Run_ImageJ module to see the ImageJ UI and all open image displays to check this). If your macro produces an image after running, you can import that image into CellProfiler by checking the "Retrieve the currently active image from ImageJ". Your macro will probably take some image as input - if it does, check the box marked "Input the currently active image in ImageJ" and select the CellProfiler image that should be ImageJ's current image when the macro starts. You then write your script in the "Macro" setting. ![]() To run Beanshell, select "Macro" in the "Run an ImageJ command or macro?" setting and select "Beanshell" as the programming language. ![]() RunImageJ is initially configured to run ImageJ commands. We hope to re-engineer this functionality for CP 3.0 and beyond- you can follow the efforts to do so here Table of Contents Note that this functionality is only fully supported up to CP 2.1.1 use of it later is at your own risk. #IMAGEJ SCRIPTING HOW TO#This page documents how to use the Beanshell scripting language to write RunImageJ scripts for ImageJ 2.0. ImageJ 2.0 comes with several scripting languages that can be used to more fully take advantage of ImageJ's capabilities. ![]()
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