Running Your Pipeline

Once you have tested your pipeline using Test mode and you are satisfied with the module settings, you are ready to run the pipeline on your entire set of images. To do this:

• Exit Test mode by clicking the "Exit Test Mode" button or selecting Test > Exit Test Mode.
• Click the " Analyze Images" button and begin processing your data sets.

During the analysis run, the progress will appear in the status bar at the bottom of CellProfiler. It will show you the total number of image sets, the number of image sets completed, the time elapsed and the approximate time remaining in the run.

If you need to pause analysis, click the " Pause" button, then click the "Resume" button to continue. If you want to terminate analysis, click the " Stop Analysis" button.

If your computer has multiple processors, CellProfiler will take advantage of them by starting multiple copies of itself to process the image sets in parallel. You can set the number of workers (i.e.,copies of CellProfiler activated) under File > Preferences...