Problem Initiating Cellprofiler headless




I am trying to run cellprofiler 3.0 headless from a java program using the command

“C:/Program Files (x86)/CellProfiler/CellProfiler.exe” -c -r -i C:/Users/Steven/Desktop/Batch/BuyoutTemp/ -o C:/Users/Steven/Desktop/Research/output -p C:/Users/Steven/Desktop/Research/Pipelines/Configuration/Config.cppipe

contained in a batch file.

when ran from standard command line, the command runs successfully with no issues. However, if i run it in an empty java project, shown below, two cell profiler instances are created but don’t pull any CPU until i manually kill the java program. Is there a reason that Cell Profiler would not run a pipeline if a parent java object is running.

package source;
import fileutil.CSVUtil;
import fileutil.CommandUtil;

public class Entry{
    public static void main(String args[]){
	    try {
            Process process = Runtime.getRuntime().exec(

        catch(Exception e) {

Any help or insight would be appreciated. Thank you!



I’ve reached out to our software engineers on this but you will also almost certainly get a faster response if post this on our GitHub instead.


Thank you, I posted the issue on the github!