Running Multiple Pipelines

The Run multiple pipelines dialog lets you select several pipelines which will be run consecutively. Please note the following:

  • Pipeline files (.cppipe) are supported.
  • Project files (.cpproj) from CellProfiler 2.1 or newer are not supported. To convert your project to a pipeline (.cppipe), select File > Export > Pipeline… and, under the “Save as type” dropdown, select “CellProfiler pipeline and file list” to export the project file list with the pipeline.

You can invoke Run multiple pipelines by selecting it from the file menu. The dialog has three parts to it:

  • File chooser: The file chooser lets you select the pipeline files to be run. The Select all and Deselect all buttons to the right will select or deselect all pipeline files in the list. The Add button will add the pipelines to the pipeline list. You can add a pipeline file multiple times, for instance if you want to run that pipeline on more than one input folder.
  • Directory chooser: The directory chooser lets you navigate to different directories. The file chooser displays all pipeline files in the directory chooser’s current directory.
  • Pipeline list: The pipeline list has the pipelines to be run in the order that they will be run. Each pipeline has a default input and output folder and a measurements file. You can change any of these by clicking on the file name - an appropriate dialog will then be displayed. You can click the remove button to remove a pipeline from the list.

CellProfiler will run all of the pipelines on the list when you hit the “OK” button.