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.

  • Open a New CP Window: (Mac only) You can run multiple instances of CellProfiler simultaneously; this is how you launch a new instance.

  • 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.