Using the File Menu

The File menu provides options for loading and saving your pipelines and performing an analysis run.

  • New project: Clears the current project by removing all the analysis modules and resetting the input modules.
  • Open Project…: Open a previously saved CellProfiler project (.cpproj file) from your hard drive.
  • Open Recent: Displays a list of the most recent projects used. Select any one of these projects to load it.
  • Save Project: Save the current project to your hard drive as a .cpproj file. If it has not been saved previously, you will be asked for a file name to give the project. Thereafter, any changes to the project will be automatically saved to that filename unless you choose Save as….
  • Save Project As…: Save the project to a new file name.
  • Revert to Saved: Restore the currently open project to the settings it had when it was first opened.
  • Import…: Gives you the choice of importing a CellProfiler pipeline file from your hard drive (From file…) or from a web address (From URL…). In either case, you can import a pipeline from a pipeline (.cppipe) file or a project (.cpproj) file. Alternately, you can import an image file list.
  • Export…: You have the choice of exporting the pipeline you are currently working on as a CellProfiler .cppipe pipeline file (Pipeline), or the image set list as a CSV (Image set listing), or the pipeline notes as a text file (Pipeline notes).
  • Clear Pipeline: Removes all modules from the current pipeline, while keeping the image file list intact.
  • View Image: Opens a dialog box prompting you to select an image file for display. Images listed in the File list panel in the Images module can be also be displayed by double-clicking on the filename.
  • Analyze Images: Executes the current pipeline using the current pipeline and Default Input and Output folder settings.
  • Stop Analysis: Stop the current analysis run.
  • Run Multiple Pipelines: Execute multiple pipelines in sequential order. This option opens a dialog box allowing you to select the pipelines you would like to run, as well as the associated input and output folders. See the help in the Run Multiple Pipelines dialog for more details.
  • Open a New CP Window: You can run multiple instances of CellProfiler simultaneously; this is how you launch a new instance.
  • Resume Pipeline: Resume a partially completed analysis run from where it left off. You will be prompted to choose the output .h5/.mat file containing the partially complete measurements and the analysis run will pick up starting with the last cycle that was processed.
  • Preferences…: Displays the Preferences window, where you can change many options in CellProfiler.
  • Quit: End the current CellProfiler session. You will be given the option of saving your current pipeline if you have not done so.